10-Year Summaries


For this 10th anniversary edition of the Lower St. Johns River Report, the Report’s authors have prepared summaries and retrospectives of the various indicators used to assess the health of the Lower St. Johns River ecosystem.  These summaries reveal a complex story of the Lower St. Johns River Basin over the past 10 years as some indicators improved while others worsened.  Additional information about these assessments are included in the main body of the Report.

I. Water Quality: Nutrients

Nitrogen: Unsatisfactory and Improving (mainstem and tributaries)
Phosphorus: Satisfactory and Improving (mainstem); Unsatisfactory and Improving (tributaries)

Description and Significance

Phosphorus and nitrogen are important and required nutrients for terrestrial and aquatic plants, including algae. Under optimal conditions, nutrients can stimulate immediate algal growth. Alternatively, if absent, nutrients can limit algal abundance. If the nutrient concentrations in a system remain high for extended periods of time, eutrophic conditions may result, potentially changing the ecosystem by favoring the growth of some organisms and changing the optimal water quality conditions for other organisms. The drainage basin for the river consists of agricultural lands, golf courses, and urban areas. Those inputs, plus effluents from municipal wastewater treatment plants and other point sources may contribute to eutrophic conditions in the LSJR. Individual homeowners may also introduce excess nutrients into the LSJR through failing septic tanks; therefore, the replacement of these septic tanks is one of the actions designated to achieve the the Total Maximum Daily Load. Sediments can act as a major reservoir of both nitrogen and phosphorus (Levine and Schindler 1992).

Ten Year Summary

From 2008 to 2015, the main stem and tributaries of the LSJR were not separated and the status of nutrients was classified as UNSATISFACTORY for the entire LSJR, with trends UNCHANGED.  Since, 2015, the main stem and tributaries of the LSJR were separately classified.  For nitrogen, the status has remained UNSATISFACTORY in both the main stem and tributaries of the LSJR based on maximum values exceeding numeric nutrient criterion (NNC) for peninsular Florida of 1.54 mg TN/L. Nitrogen concentrations in the LSJR have been IMPROVING since 2013, likely due to the TMDL efforts beginning in 2008 as well as others, specified below and in the Nutrients section.

From 2008 to 2015, the status of phosphorus in the mainstem and tributaries of the LSJR was UNSATISFACTORY, based on the maximum values exceeding the NNC value of 0.12 mg TP/L.  In the 2016 report, the STATUS of phosphorus in the mainstem changed to SATISFACTORY and has remained SATISFACTORY in 2017 with the trend of conditions IMPROVING.  The tributaries of the LSJR still have a status of UNSATISFACTORY; however, as of 2017, the trend has changed to IMPROVING.

Future Outlook

Since 2008, Basin Management Action Plans have established restoration strategies with the goal of reducing nutrient loading into the SJR to meet TMDL guidelines. Government agencies are working with municipal and industrial wastewater treatment facilities and NPDES permitted facilities to reduce nutrient loadings from permitted discharges. Also, nutrient-rich waters coming from standard secondary water treatment plants may be recycled and used for irrigation. Local utilities and government agencies have worked to reduce nutrient discharges since 2000 including a large public outreach campaign to reduce fertilizer use in residential landscapes. Government agencies have been working with farming and silviculture operations to implement best management practices to reduce and treat runoff of nutrients. The reduction and treatment of urban storm water runoff by Municipal Separate Storm Sewer Systems (MS4), improvement of development design and construction by commercial developers and homebuilders, and restoration projects by federal, regional, and state agencies may all influence the attainment of projected future goals of the TMDL program.

II. Water Quality: Algal Blooms

Status and Trend: Unsatisfactory and Unchanged

Description and Significance

Phytoplankton comprise a variety of microscopic plants species (including cyanobacteria, also known as blue-green algae) that serve as the base of the food chain and are found in healthy rivers and lakes. Under certain conditions, these organisms can multiply rapidly, resulting in very high concentrations of the algae and creating what is called a “bloom.” These blooms can have significant impacts on the local ecology of a river, lake, or estuary.

Algal blooms are often described as nuisances because of the odor and unsightliness of algal scum and the green water that often accompanies them, but the potential impacts go well beyond being a nuisance. Blooms often induce high oxygen production during the daylight hours (due to photosynthesis), followed at night by very low oxygen levels (due to respiration). These blooms can become so dense that sunlight cannot reach the native submerged aquatic vegetation, reducing those plants’ ability to photosynthesize and to grow. When the bloom biomass decays, dissolved oxygen levels are decreased. As a consequence, survival of juvenile fish and other aquatic organisms may become threatened by low oxygen and reduced food and habitat caused by algal blooms and mats.

Nutrients in the water are the driving factor for algal blooms, while warm temperatures, sunlight, and water flow also contribute to the speed that free-floating algae grow and accumulate in lakes, ponds, rivers, and streams. As these phytoplankton are normally found in water (even in the absence of an algal bloom), chlorophyll-a values are used to monitor relative phytoplankton abundance.

Ten Year Summary

Over the past ten years, the status and trends of algal blooms has been UNSATISFACTORY. From 2013-2017, trends were UNCHANGED after having been rated as WORSENING between 2008-2012. In general, the data do not show overall reductions of chlorophyll over the past 10 years, and the occurrence of yearly blooms, as well as larger ones in 2010, 2013, and 2016 may indicate that they may not decrease any time soon. For example, in 2010, the freshwater section of the river experienced massive cyanobacterial algal blooms (Littlepage 2010), and over half of the chlorophyll-a samples in the FDEP STORET database for that year had levels that signify potential bloom levels (40 ug/L), suggesting significant ecological impact. Furthermore, the marine/estuarine portion of the river also had elevated algae levels. In 2013 and 2016, the LSJR also experienced highly visible blooms that had high toxin levels produced from the algae (Schoettler 2013; Scanlan 2016). However, the FDEP has conducted additional research at Racy Point, a particularly algal bloom prone location in the St. Johns River, and has reported a decrease in the number of days that the location experienced algal blooms from 1995 to 2013.

Future Outlook

Decreasing the amount of nutrients is the key to decreasing algal blooms, and considerable progress has been made in decreasing the amounts of nutrients that otherwise would have gone into the basin.  However, the effectiveness of current efforts to reduce nutrient loading of the LSJR at decreasing the frequency and duration of algal blooms will not be known for several years, and other factors (such as changes in the short-term and in the long-term changes of salinity and water temperature) will also influence the prevalence of algal blooms.

Unfortunately, the database (which contains the chlorophyll data used to assess algal blooms) does not fully represent the actual state of the river in that some blooms are not sampled and analyzed, and thus are not figured into hard numbers that are used to determine the health of the river.  We know from witnessing them, that algal blooms occur, and neither make the news nor are represented in the database.

III. Water Quality: Salinity

Status and Trends: Unsatisfactory and Worsening

Description and Significance

Salinity deals with the chemistry of the intermixed seawater and freshwater in the St. Johns River, or in any estuary for that matter.  Changes in salinity within the St. Johns River are not due to chemical changes of the waters, but rather are the consequence of physical factors that enable more or less saline (ocean-derived) waters to enter into the river. Two primary factors are responsible for physically modifying salinity in the river:

  • OCEAN: Tides, storm surge and sea-level rise
  • HYDROLOGY: Rainfall and watershed runoff and routing

The OCEAN factors predominate salinity changes in the river, while HYDROLOGY is a supplemental factor.  Large spring tides combined with storm surge generate ephemeral increases in river salinity.  Sea-level rise permits a gradual increase in the baseline level of river salinity due to the steady influx of saline waters into the estuary.  Low precipitation (drought periods) allows the ocean-based seawater to push further upstream into the river, which can persist for months, and as long as years in some cases.  These natural factors of OCEAN and HYDROLOGY constitute the primary cause for salinity changes in the St. Johns River, where salinity is trending upward.

Ten Year Summary

Salinity was first covered in the SJR Report in year 2014.  In this 10-year update of salinity in the St. Johns River, a ten-year-long historical record of salinity data covering 1996–2006 is compared with a recent salinity dataset spanning over year 2016, for Dames Point, situated at river km 20 (see Figure 10Yr-1 for station location).  As a disclaimer, salinity data were not collected for the period of 2006–2016, whereby the comparison of year 2016 to the ten-year record of 1996–2006 represents just one single year (2016) versus a longer-term record (ten years: 1996–2006).

Figure 10Yr-2 displays the salinity data for 1996–2006 versus 2016.  The historical (1996–2006) data are shown as an envelope, where the ‘middle’ curve represents the typical value (mean) of salinity and the ‘high’ and ‘low’ curves represent the typical range (maxima and minima) of salinity.  The present-day (2016) data are shown as a curve of the measured values.  Some observations are noted, which are founded upon the following tabulation of comparisons (2016 relative to 1996–2006):

If greater than max If less than min If greater than mean If less than mean
11.8% 0.4% 51.2% 48.8%

Approximately 12% of the time, salinity for year 2016 surpassed the maxima associated with the historical (1996–2006) record.  Conversely, salinity for year 2016 was below the historical minima less than 1% of the time.  Present-day salinity exceeded the typical (mean) value of historical salinity about 51% of the time (the opposite was the case ~49% of the time).  The results suggest that present-day salinity in the St. Johns River is generally greater than the historical basis (10 to 20 years prior) of salinity.

Figure 10Yr-1
Figure 10Yr-1. Station location of Dames Point (river km 20).
Figure 10Yr-2
Figure 10Yr-2. Salinity for 1996–2006 versus 2016.

Summary Statement

The results suggest that present-day salinity in the St. Johns River is generally greater than the historical basis (10 to 20 years prior) of salinity.

IV. Water Quality: Turbidity

Status and Trend: Satisfactory and Unchanged

Description and Significance

Turbidity is a measure of the optical clarity of a liquid: the more cloudy the liquid, the more turbid it is. The implications of high turbidity for a natural waterbody include less light penetrating the water column to reach rooted submerged plants and thus hinder aquatic photosynthesis. This has a large impact on animals, which depend on the grasses for food and shelter.

Rainfall and drought can affect turbidity strongly. Because the LSJR is a black water system, high rainfall events can increase turbidity by moving tannin-laden waters into the main stem and tributaries. Drought can cause a reduction in turbidity, because with less rainfall and stormwater runoff, the contribution of spring flows to the river increases the proportion of clear water in the system.

Ten Year Summary

In the early years of this Report, mainstem and tributary conditions were separated, and while the main stem was SATISFACTORY, the tributaries were rated as UNSATISFACTORY. These conditions are perceived to be improving. In 2010, the entire basin was taken under one rating, which was UNSATISFACTORY until 2014. In 2014, the mean turbidity value reached its lowest level since 1997, and the percentage of data points above the water quality criterion was at its lowest level (0.40%). SATISFACTORY conditions have continued and remained UNCHANGED since 2014, and in 2016 the maximum value reported was one of the lowest maximum values reported since 1997.

Future Outlook

Current management of turbidity in Duval County, for example, includes a requirement for land-disturbing (e.g., land clearing, dredge and fill, and construction) activities to be overseen by a developer’s certified staff, routine visits of land-disturbing sites, review of erosion control plans, and a citizen reporting mechanism. Heightened public awareness and improved engineering sediment control practices are bringing improvements in this area.

Vigilance in design of retention and detention ponds, sediment fences and public monitoring all can keep turbidity low in the LSJR. Reporting of turbidity events and sediment discharges near land-clearing and construction projects, particularly future Developments of Regional Impact (DRI) and monitoring existing municipal separate storm sewer system (MS4) areas for storm runoff should help ensure the best outcomes for the LSJR.

V. Aquatic Life: Submerged Aquatic Vegetation (SAV)

Status and Trend: Unsatisfactory and Uncertain

Description and Significance

SAV found in the LSJRB are primarily freshwater and brackish water species. Commonly found species include tape grass (Vallisneria americana), water naiad (Najas guadalupensis), and widgeon grass (Ruppia maritima). Tape grass forms extensive beds when conditions are favorable. The greatest distribution of SAV in Duval County is in fresher waters south of the Fuller Warren Bridge. Rapid regeneration of grass beds occurs annually in late winter through September when water temperatures become more favorable for plant growth. Submerged aquatic vegetation in the tannin-rich, black water LSJR is found exclusively in four feet or less of water depth. Poor sunlight penetration prevents the growth of SAV in deeper waters.  SAV requires more light in a higher salinity environment because of increased metabolic demands (Dobberfuhl 2007). During drought conditions with reduced stormwater runoff, there is an increase in light availability and lower turbidity that can result in epiphytic organisms growing on the surface of the grasses and possibly causing competition for light with SAV.

SAV is important ecologically and economically to the LSJRB. SAV persists year-round in the LSJRB and forms extensive beds, which carry out the ecological role of “nursery area” for many important invertebrates, and fish. Also, aquatic plants and SAV provide food for the endangered West Indian manatee Trichechus manatus. Commercial and recreational fisheries, including largemouth bass, catfish, blue crabs and shrimp, are sustained by healthy SAV habitat (Watkins 1992). Jordan 2000 mentioned that SAV beds in LSJRB have three times greater fish abundance and 15 times greater invertebrate abundance than do adjacent sand flats. Sagan 2006 noted that SAV adds oxygen to the water column in the littoral zones (shallow banks), takes up nutrients that might otherwise be used by bloom-forming algae (see Section 2.4 Algal Blooms) or epiphytic alga, reduces sediment suspension, and reduces shoreline erosion.

Ten Year Summary

The SJRWMD conducted year-round sampling of SAV from 1998 to 2011 at numerous stations (about 152 stations along line transects of the St. Johns River (1.25 miles apart)) (Hart 2012). This monitoring program, which included water quality data collected at SAV sites, was suspended due to budget cuts, so no new data were available from 2012-2014. Sampling resumed on a more limited basis in 2015 and 2016 and include fewer stations (Jacksonville to Black Creek/Hallows Cove, about 40 stations). Reduced sampling frequency and coverage has led to much of the uncertainty associated with trend analysis.

Over the longer-term (2001-2011), there was a declining trend in grass bed length (Appendix The degree to which this occurred was greater north of the Buckman Bridge compared to south of the bridge. North of Buckman Bridge the average grass bed length declined from 139 m (1998) to 22 m (2011). When sampling was resumed in during 2015 and 2016, the average grass bed length was 54 m. Similar trends were observed in the other grass bed parameters to varying degrees including (1) mean bed length (includes bare patches) and grass bed length (excludes bare patches), (2) total percent cover by SAV (all species), and (3) Vallisneria percent cover (see Table 1 in Appendix In addition, anecdotal observations from a manatee aerial survey of the area in May 2017 indicated that grass bed coverage north of the Buckman Bridge (Bolles School to Buckman-east bank) and some parts from NAS JAX to Buckman (west bank) was bare. This was most likely due to the lack of rainfall over the past year that resulted in increased salinity conditions in that part of the river contributing to the decline in grass bed coverage.

South of the Buckman Bridge to Hallows Cove, the average grass bed length was variable but showed less decline than trends observed north of the bridge. Average grass bed length declined from 106 m (1998) to 89 m (2011), with a maximum of 146 m in 2004 when four hurricanes skirted Florida providing above average rainfall and fresher conditions prevailed. When sampling resumed during 2015/16, the average grass bed length was 81 m. Similar trends were observed in the other grass bed parameters to varying degrees including (1) mean bed length (includes bare patches) and grass bed length (excludes bare patches), (2) total percent cover by SAV (all species), and (3) Vallisneria percent cover (see Table 2 in Appendix Moreover, anecdotal observations from a manatee aerial survey of the area in May 2017 indicated that grass bed coverage south of the Buckman Bridge to Black Creek (east bank) and Switzerland (west bank) supported relatively lush grass beds compared to the north. This was most likely due to lower salinity and fresher conditions prevailing in this part of the river compared to the north.

As a result, the status of SAV was rated as UNSATISFACTORY and trends as UNCERTAIN. There were no new data for the areas of the river south of Hallows Cove to Lake George, including Crescent Lake in 2015/2016.

Future Outlook

Continuation of long-term monitoring of SAV is essential to detect changes over time. Grass bed indices, along with water quality parameters, should be used to determine the current state of health. They can then be used to identify restoration goals of the SAV habitat, which will preserve and protect the wildlife and people who rely on the habitat for either food, shelter, or their livelihood.

The grass beds monitoring program should be resumed and expanded as soon as possible especially in light of efforts to further deepen the port channel, and the pending environmental and habitat changes that are likely to ensue as a result of global warming, rising sea levels, El Niño events, and storms.

Learning more about SAV response to drought and/or periods of reduced flow can provide crucial understanding as to how water withdrawals (including broader water supply policy), dredging, and the issue of future sea level rise will affect the health of the ecosystem by adversely altering salinity profiles.

VI. Water Quality: Dissolved Oxygen

Status and Trend: Satisfactory and Improving (mainstem); Unsatisfactory and Unchanged (tributaries)

Description and Significance

Dissolved oxygen (DO) is defined as the concentration of oxygen that is soluble in water. Many factors affect DO, such as temperature, salinity, sediments and organic matter from erosion, runoff from agricultural and industrial sources, wastewater inputs, and excess nutrients from various sources. In general, the more organic matter in a system, the less DO available. DO concentration is important for supporting aquatic life. Animals survive within a narrow range of DO concentrations in aquatic systems and DO concentrations below 4 mg/L can be detrimental for many organisms.

Ten Year Summary

From 2008 to 2013, the status of DO in the entire LSJR was UNSATISFACTORY with an UNCHANGED trend. From 2014 to 2017, the DO in the main stem and tributaries were evaluated separately. Both the main stem and tributaries had DO values that were UNSATISFACTORY, based on comparisons to the reference values discussed below and in the Water Quality Section. Since 2016, the status of DO in the main stem changed to SATISFACTORY; however, the DO in the tributaries remains UNSATISFACTORY. It should be noted that this change in DO status in the main stem was in part due to changes in DO water quality criteria guidelines and reference values (see below). In 2017, the trend in the main stem changed to IMPROVING, which is likely due in part to efforts to meet the TMDL (see Nutrients section).

Until 2013, the class III Freshwater Quality Criterion (WQC) for DO has been 5.0 mg/L (62-302.530, F.A.C.; DEP 2013d), requiring that normal daily and seasonal fluctuations must be maintained above 5.0 mg/L to protect aquatic wildlife. The Florida DEP developed site specific alternative criteria (SSAC) for the predominantly marine portion of the LSJR between Julington Creek and the mouth of the river, which requires that DO concentrations not drop below 4.0 mg/L. DO concentrations between 4.0 and 5.0 mg/L were considered acceptable over short time periods extending up to 55 days, provided that the DO average in a 24-hour period was not less than 5.0 mg/L (DEP 2010h).

In April, 2013, the U.S. EPA approved new DO and nutrient related water quality standards to be adopted by the Florida Environmental Regulation Commission (ERC). Under the new revisions, in predominantly freshwaters of the SJR, the DO should not be less than 34% saturation, which is equivalent to approximately 2.6 mg/L at 30°C and 3.09 mg/L at 20°C (DEP 2013d). Additionally, in the portions of the LSJR inhabited by Shortnose or Atlantic Sturgeon, the DO should not be below 53% saturation, which is equivalent to approximately 4.81 mg/L at 20°C, during the months of February and March. After much assessment, the FDEP supported that maintaining the 5.0 mg/L minimum DO criterion in the location where spawning would occur should “assure no adverse effects on the Atlantic and shortnose sturgeon juveniles.”

For predominantly marine waters, minimum DO saturation levels shall be as follows:

“1. The daily average percent DO saturation shall not be below 42 percent saturation in more than 10 percent of the values; 2. The seven-day average DO percent saturation shall not be below 51 percent more than once in any twelve week period; and 3. The 30-day average DO percent saturation shall not be below 56 percent more than once per year.”

For more information, please refer to the U.S. EPA decision document (EPA 2013dEPA 2013).

Additionally, seasonal limits for Type 1 SSAC were implemented in February 2014 for certain areas of the LSJR, where the default criteria in Rule 62-302.530, F.A.C. would apply during the other times of the year. For the Amelia River, the segment between the northern mouth of the river and the A1A crossing, a SSAC for DO has been set to 3.2 mg/L as a minimum during low tide from July 1st through September 30th, and not below 4.0 mg/L during all other conditions.  Likewise, Thomas Creek has a SSAC for DO of 2.6 mg/L, with no more than 10 percent of the individual DO measurements below 1.6 mg/L on an annual basis.

Since 2016, we used the 30-d average DO percent saturation value of 56%, which is the most conservative, as a reference value to compare to the data from the marine/estuarine portion of the LSJR. This value is equivalent to approximately 5.09 mg/L at 20°C and 4.28 mg.

Future Outlook

Analysis of available data indicates that the average DO levels in the LSJRB are generally within acceptable limits; however, unacceptable DO concentrations occurred intermittently during every month of every year prior to 2015. Low DO was most problematic during summer months with many of the lowest measurements occurring in tributaries. Nutrient reduction strategies have recently been devised by government agencies and appear to have helped increase DO concentrations in the LSJR to some extent. Additionally, monitoring agencies are now making efforts to collect data that better represent the variable DO conditions and to concurrently document other important water quality characteristics for an improved assessment of the river’s health.

VII. Water Quality: Bacteria (Fecal Coliform)

Status and Trends: Uncertain (mainstem); Unsatisfactory and Unchanged (tributaries)

Description and Significance

Fecal coliform bacteria are part of normal, healthy digestive systems in birds and mammals, and exit the body in feces.  These bacteria, if found in waterways, are themselves not considered harmful, but can serve to indicate that human waste has recently entered the waterway.  On the other hand, when people are ill with other types of microorganisms that are infectious (mainly viruses and bacteria), their feces will contain these harmful pathogens in addition to the fecal coliform bacteria.  Protecting waterways from pathogens is important to prevent illnesses to wildlife and humans that interact with the water.  Since it would be impossible to test waterways for all possible pathogens, fecal coliforms are used as indicators of recent human sewage since they are ubiquitous in human feces.

Fecal coliform bacteria end up in natural waters by a variety of ways attributable to humans, such as sanitary sewer overflows, failing septic tanks, and animal waste run off from animal agriculture and uncurbed cats and dogs.  Fecal coliform bacteria also reach waterways from natural sources such as free-roaming wildlife and birds.

Ten Year Summary

For all ten years of this Report series, the status of fecal coliform bacteria in St. Johns River tributaries has been rated UNSATISFACTORY due to fecal coliform numbers that have been persistently higher than the water quality criteria.  Twenty-five of the tributaries are under Basin Management Action Plans (BMAPs), which involves identifying and remedying sources of fecal contamination.  Many tributaries have shown improvement over the years, as noted by the trend ratings of IMPROVING in 2011, 2012, 2013, and 2015, and many individual tributaries have undergone significant reductions of fecal coliform concentrations over the last ten years (Table 2.2). However, overall tributary conditions continue to remain well above water quality criteria, despite some successes and years of effort to reduce these levels via BMAP activities, and the trends have been UNCHANGED for the past couple of years.

Because the primary sources of fecal coliform are stormwater, wastewater, and septic tanks, the projects undertaken to reduce fecal coliform usually address these types of water streams, such as wastewater infrastructure and treatment improvements, construction of stormwater retention ponds, removal of illicit wastewater connections to waterbodies, and septic tank phaseout and replacement by connection to municipal sewage services. Yet despite these projects, most tributaries remain significantly impaired for fecal coliform. Stakeholders have conducted an intensive effort to investigate continued sources of fecal coliform.

The main stem of the St. Johns River was rated SATISFACTORY during the first two years of the Report (2008 and 2009), based on data from the FDEP “River-at-a-Glance” program.  These data showed the main stem largely in compliance for both years (Appendix 2.6.1).  Since the tributaries were largely not in compliance, the sampling of the mainstem was discontinued and the focus became the tributaries.

Future Outlook

Future long-term efforts generally involve maintenance activities, modified or expanded inspections, educational outreach, and basin-specific cleanup strategies.  The continued high levels of fecal coliform in tributaries is truly a puzzle to solve since potential sources are not obvious. Since some coliform bacteria continue to grow and reproduce in waterways long after the threat of human pathogens is gone, determining whether locations have resident populations of fecal bacteria that are not indications of recent human sewage is important.  The FDEP and the COJ are continuing to develop a source identification program to try to sort out sources of human fecal bacteria vs. animal fecal bacteria since pathogens from human waste are generally more dangerous than those from wildlife, livestock, and pet wastes.  This program relies on detecting manmade compounds such as acetaminophen (Tylenol) and the sweetener sucralose (Splenda) as well as the genetic signatures from human bacteria in waterways with high fecal bacteria.

In 2016, the FDEP adopted 2012 USEPA criteria (EPA 2012b) that uses E. coli as fecal indicator bacteria in freshwater, and enterococci as fecal indicator bacteria in marine waters, as opposed to using the older, more general fecal coliform bacteria criteria for both fresh and marine waters.  Water testing to adhere to these new criteria are being phased in, and the new criteria reflect a better correlation between swimmer illnesses compared to fecal coliform, which can include bacteria whose numbers do not correlate with illness.

VIII. Water Quality: Contaminants

Status and Trends:
Sediment PAHs: Unsatisfactory, Improving in the Northern section and Worsening in the Southern section

Sediment PCBs, pesticides, metals: Unsatisfactory and Unchanged

Water column metals: Mixed/Unchanged, Improving in the mainstem and Incertain in the tributaries

Description and Significance

Contaminants are chemicals that are found at elevated concentrations in the environment. Some are produced solely by human activity, but many occur naturally in small quantities. Both anthropogenic (human-made) and naturally occurring compounds may become toxic when they are introduced into ecosystems at elevated concentrations, often as a result of human activity (i.e., polyaromatic hydrocarbons, polychlorinated biphenyls, metals). Concentrations of naturally-occurring compounds often vary with local geology and environment. Thus, it is much more difficult to detect human input and harmful concentrations for naturally occurring compounds than for those that are produced solely by human activity.

Contaminants can reside in water, sediments, and biota (i.e., animals and plants). The sediments of rivers often serve as reservoirs for chemical contaminants. Plants and animals that live in sediments (benthic organisms) are potentially exposed to both contaminated water and sediments, so assessments of their toxic responses to contaminants are particularly important in determining overall river health.

Chemicals in four environmentally significant categories are evaluated in this report. The categories include 1) polyaromatic hydrocarbons (PAHs), 2) metals (in the water column and sediment), 3) polychlorinated biphenyls (PCBs), and 4) pesticides. These chemicals vary in their chemical structure, their sources, and their specific fates and effects, but they all have a high potential for prevalence, persistence, toxicity and bioaccumulation.

Ten Year Summary

For the past 10 years, the PAH concentrations in the LSJR have had a status of UNSATISFACTORY.  Generally, in the Northern section of the LSJR the trend of the conditions has been IMPROVING and in the Southern section the trend of the conditions has been WORSENING.

Like PAHs, both PCBs and pesticides in the LSJR have had a status of UNSATISFACTORY since 2008 and the trend has remained UNCHANGED.

When the report began in 2008, we evaluated metals in the sediments only; in 2013, we also began evaluating metals in the water column (including arsenic, copper, cadmium, lead, nickel, silver, and zinc).  The metals in the sediments have had a status of UNSATISFACTORY and a trend of UNCHANGED for the past 10 years.  Metals in the water column have had a status of MIXED, where certain metals were SATISFACTORY and others, such as copper, were UNSATISFACTORY. The trend for metals in the water column has been UNCHANGED for all years except this year. The current status of metals in the water column of the LSRJ mainstem is now SATISFACTORY with a trend of IMPROVING. This reduction in metal concentration in the water column is likely associated with reduced inputs and may reflect the recent efforts associated with TMDLs. The status and trend of metal concentrations in the tributaries of the LSJR cannot be determined because of the lack of data, and is therefore UNCERTAIN. The data set for metals in the water column has been substantially reduced over the years, which limits trend analyses.

Contaminant concentrations in the sediments of the LSJR remain elevated, and data for all of these contaminants has become more limited over the years.

Future Outlook

Several of the tributaries have shown severe contamination over the years.  The large Cedar-Ortega basin is of particular concern as it has repeatedly exhibited among the highest levels and frequencies of contamination over the years.  It has been recognized at least since 1983 that the large, complex network of tributaries is burdened by years of discharges of wastewaters and runoff from small, poorly managed industries, and from identified and unidentified hazardous waste sites. The Cedar-Ortega basin also suffers from its location in the middle of the LSJR, where the transition between riverine and oceanic inputs promotes sedimentation and reduces flushing. These factors produce a highly stressed system. However, recent construction of a stormwater treatment facility on the Cedar River could improve the situation in that area.

Rice Creek is another western tributary of the LSJR that has exhibited long-term pressure from a variety of contaminants and it has often had the highest contaminant concentrations in the region. Relocation of the discharge of a pulp and paper mill effluent from the creek to the mainstem in 2013 will have an unknown impact on the sediment contaminants discussed.

Outside of the areas of highest concern, contaminants act as underlying stressors all throughout the basin. Even the relatively pristine south mainstem portion of the LSJR has contamination that may affect sensitive organisms. Overall, the mass of contaminants released to the atmosphere from point sources in the LSJR region has significantly declined over a decade. However, little change in surface water discharges has occurred and there have been significant increases in discharges of some metals. Water concentrations of several metals have generally declined in the last few years in the mainstem and are generally below water quality criteria. However, as stated above, the metal concentrations in the tributaries may be problematic to aquatic life.  Additionally, sediments act as a reservoir as well as a source (if disturbed) of contaminants. Continued efforts are needed to reduce pollutant loadings through stormwater control projects, permitting, and best management practices.

IX. Aquatic Life: Macroinvertebrates

Status and Trend: Uncertain

Description and Significance

Benthic macroinvertebrates are small animals that live on or in the sediment of the LSJRB that are an important component of the river’s food web. This taxonomic group includes crabs, snails, shrimp, clams, insects, polychaetes, nemerteans, platyhelminthes, and barnacles. They are prey to commercially and recreationally important fish and invertebrate species (see Threatened & Endangered Species and Finfish sections). Benthic macroinvertebrates are also important for turning over the sediment (bioturbation) which aids in oxygenating the sediment and changing the composition of grain sizes. In addition, members of this group can serve as indicators of environmental stress, including temperature, salinity, pollutants.

Ten Year Summary

The status of macroinvertebrates was UNSATISFACTORY from 2008-2012 due to the presence of pollution-tolerant species and UNCERTAIN from 2013 to present due to a lack of data. Similarly, trends remain UNCERTAIN without fine-scale studies of diversity and abundance. Changes in water quality parameters, including salinity concentrations, water temperatures, and flow rates, can influence macroinvertebrate communities and trophic relationships.

Future Outlook

The paucity of consistent monitoring programs through the LSJRB, complicated by natural high spatial and temporal variability prevent a comprehensive understanding of the status of macroinvertebrates in the LSJRB. However, the few studies made available indicate pollution and disturbance-tolerant species are prevalent and decreasing aquatic insects have also been observed since the 1970s. What is further unclear is how communities will respond with salinity, temperature, and water chemistry (nutrients, pollutants) changes.

X. Aquatic Life: Finfish

Status and Trend: Mixed

Description and Significance

Baitfish: Baitfish are most important in the food web as prey for a number of larger fish species. They are also important as omnivores that recycle plant and/or animal material that is then available for higher trophic levels. Recreationally the fish are used for bait for fishing, whereas commercial uses include products, such as fertilizers, fishmeal, oil, and pet food.

Atlantic Croaker: The Atlantic croaker is a bottom-dwelling predator that is commonly encountered around rocks and pilings in estuarine habitats. They feed on small invertebrates, and are fed on by red drum, seatrout, and sharks. For many years, their commercial fishery has been one of the biggest in the LSJR. Additionally, they are recreationally caught for their food value. Recreationally, they can be caught all months of the year.

Blue Crab: Blue crabs are very important in both the benthic and planktonic food webs in the St. Johns River. They are important predators that can affect the abundance of many macroinvertebrates, such as bivalves, smaller crabs, and worms. They are also important prey for many species. Smaller crabs provide food for drum, spot, croaker, seatrout, and catfish, while sharks and rays eat larger individuals. A strong recreational blue crab fishery exists, although there are relatively few data on it. The blue crab fishery is the largest commercial fishery in the LSJRB.

Channel & White Catfish: Channel and white catfish are omnivorous fish that are very important in benthic food webs in the more freshwater sections of the LSJR. They are a major component of the freshwater commercial fishery in Florida. There is also a large recreational catfish fishery within the river. Channel catfish are often stocked in ponds and lakes to maintain population numbers.

Largemouth bass: Largemouth bass are predatory fish that occupy shallow brackish to freshwater habitats south of the Buckman Bridge. They are carnivores feeding on zooplankton, insects and crustaceans, including crayfish, frogs, and salamanders. Recreationally, bass are a popular game fish in the area for visiting and local anglers.

Mullet: Striped mullet (also known as black mullet) are detritivores that have a wide salinity range. Mullet migrate offshore to spawn with their resultant larvae eventually drifting back to coastal waters and marsh estuaries. They are abundant and significant in the transfer of energy from the detrital matter they feed on to their predators such as birds, seatrout, sharks, and marine mammals. The commercial mullet fishery has been the largest among all fisheries in the St. Johns for many years with over 100,000 lbs. harvested annually. Additionally, mullet are sought after recreationally for their food and bait value.

White, Pink, and Brown Penaeid Shrimp: White, pink, and brown shrimp penaeid shrimp exist within the estuaries and nearshore waters of the northeast Florida region. The white shrimp is the most common species in local waters. All three are omnivorous feeding on worms, amphipods, molluscs, copepods, isopods and organic detritus.  In their post-larvae and juvenile stage, they are important prey for sheepshead minnows, insect larvae, killifish, and blue crabs. As adult shrimp, they are preyed on by a number of the finfish found within the river.

The LSJR supports both recreational and commercial shrimp fisheries. The recreational fishery is likely to be large although there is relatively little information on it. In contrast, the commercial shrimp fishery is one of the largest fisheries in the region. However, most shrimp obtained for human consumption are caught by trawlers offshore. Commercial trawling in the LSJR represents a much smaller fishery.

Red Drum: Red drum are predatory fish that are found in the estuarine sections of the St. Johns River. They are bottom feeders that eat crabs, shrimp, worms, and small fish. Their predators include larger fish, birds, and turtles. A strong recreational fishery exists for red drum. Red drum has not been commercially harvested since 1988 to minimize impacts to natural populations. In spite of that, FWC data indicate a decreasing trend in the adult fish.

Sheepshead: Sheepshead are common nearshore and estuarine fish that are very often associated with pilings, docks and jetties. They have an impressive and strong set of incisor teeth that are used to break apart prey, such as bivalves, crabs and barnacles. They are fed on by larger predators such as sharks and marine mammals. The commercial fishery is one of the larger ones within the river. Recreationally, sheepshead are valued by fisherman in the area for their high food value. They can be caught all months of the year.

Southern Flounder: The southern flounder is common in and around inshore channels estuaries associated with the St. Johns River. It is a bottom-dwelling predator that feeds on shrimp, crabs, snails, bivalves, and small fish. They are preyed on by sharks, marine mammals, and birds. The commercial flounder fishery is one of the larger ones in northeast Florida. Flounder are also highly sought after recreationally for their excellent food value.

Stone Crab: The stone crab is a fairly common benthic predator that inhabits hard bottoms (such as oyster reefs) and grass beds in the northeast Florida area. Stone crabs are opportunistic carnivores feeding on oysters, barnacles, snails, clams, etc. As larvae in the plankton, they are preyed on by filter-feeding fish, larval fish, and other zooplankton. As adults, they are preyed on by many larger predators in the river.

The stone crab commercial fishery is relatively new and small in the LSJR. The highest number of claw landings within the river basin likely comes from Duval County. Claw landings from other counties of the LSJR most likely come from collections made in the ICW.

Spotted Sea Trout: The spotted seatrout is a bottom-dwelling predator that is common in estuarine and shallow coastal habitats in northeast Florida. It is a carnivore that preys on a number of small fish species, such as anchovies, pinfish and menhaden. A number of predators feed on seatrout, including Atlantic croaker, cormorants, brown pelicans, bottlenose dolphin, and sharks. There are recreational and commercial spotted seatrout fisheries within the St. Johns River.

Ten Year Summary

Data provided by the Florida Fish and Wildlife Research Institute (FWRI) include Commercial fisheries landings reports (1994-2016) and data from the Fisheries Independent Monitoring (FIM) program (2002-2016). For commercial landings data, there are uncertainties associated with either the exact location of where a fish was caught and/or the method of estimating total number of landings for a given area. In particular, these data do not differentiate between fish and invertebrates caught in the LSJR or the Intracoastal Waterway, leading to some uncertainty in the status and trends observed.

UNCERTAIN status and UNCERTAIN trends

Blue Crab: Commercial landings of blue crabs have been variable, but trending downward for north and south sections of LSJR from 1986 to 2016. Additionally, more landings occur in the southern versus northern section of the river (Appendix 3.3.2a). There was a significant percent reduction in landings for blue crabs over all during the past decade (65% in 2016) compared to an average of 75% (range 61%-86%).

A strong recreational blue crab fishery exists, although there are relatively few data on it. The primary limitation with the commercial landing data is that it does not account for young crabs that are too small to be harvested. Additionally, there may be uncertainties regarding location of where the crabs are collected. There is uncertainty associated with the maximum age of blue crabs in Florida.

Southern Flounder: Commercially, total flounder landings have decreased significantly for the north river section and increase in the southern section of the river (Appendix 3.2.8a). However, the commercial catch per trip increased in the northern section of the river and a decrease in the southern section of the river. No significant change has occurred in this trend in the last 10 years (2008-2016).

White, Pink, and Brown Penaeid Shrimp: Generally, penaeid shrimp are very abundant in the region. The season is closed during April and May in Nassau, Duval, St. Johns, Putnam, Flagler, and Clay Counties. There have been drastic fluctuations among the years with peak landings occurring in 2004. Less fluctuation has occurred in recent years, but the catch per trip has also decreased significantly particularly in the north section of the river where more bait shrimp are reported.


Largemouth bass: Over the past ten years, the status of largemouth bass was UNCERTAIN with UNCHANGED trends. FWRI research in the past 10 years shows similar yearly abundances from 2005 to 2015. There is not enough information to assess the status of the recreational fishery associated with largemouth bass in the lower St. Johns River. However, they are not likely to be overfished soon.

Sheepshead: Since 2009, the status of sheepshead was UNCERTAIN with UNCHANGED trends. In 2008, the status was SATISFACTORY. Total landings over time showed a declining trend, as did landings per trip in both north and south sections of the river (Appendix 3.2.9a). It should be noted that data from the southern counties most likely include a significant number of fish caught in the ICW. Sheepshead are common in the St. Johns River with populations that not at risk from overfishing.

Channel & White Catfish: Over the past ten-years catfish landings have improved slightly, however, the long-term trend is WORSENING. As a result, the status is UNCERTAIN, and the future is uncertain. Primary abundances occur in the more freshwater reaches of the river south of Buckman Bridge. Since the late 1990’s, landings have been decreasing in the north (landings mostly likely from tributaries in this area) sections of the river (Appendix 3.2.6a). In addition, the gear used targeted the small fish and limited data exists about the adults.

SATISFACTORY status and UNCHANGED trends: Baitfish, Atlantic Croaker, Red Drum, Stone Crab, Spotted Sea Trout

Atlantic Croaker: Commercially, total landings from 1986-2016 have increased for the northern section of the river and whole river, however, most of the rebound has occurred from 2007 to 2016. However, catch per trip also had an increasing trend for the north, south and whole river, but this was not statistically significant. In both sets of commercial data, landings are lower in the southern sections of the river (Appendix 3.2.10a).

Baitfish: While landings of baitfish have remained temporally consistent, the catch per landing showed significant decreasing trends for the north section of the river, but was not significant for the south river section. Further, baitfish landings seem to be higher in the southern sections of the river. More recently, from 2007 to 2016, catch per trip showed significant increasing trend for the whole river.

Stone Crab: From 2007 to 2016 landings have increased although the amount caught per trip has decreased. Crab claws are more likely caught in the Intracoastal Waterway of the more southern counties than in the river itself. Stone crabs are not currently at risk of being overfished but are probably at the maximum level of landings that can be harvested under current conditions.

Spotted Sea Trout: Landings have generally remained variable but consistent for the whole river. 


Mullet: Over the past ten years, the status of mullet was SATISFACTORY with UNCHANGED trends from 2008-2016. In 2017, trends were IMPROVING. Commercial landings and landings per trip have showed an increasing trend for the period 2007-2016 in both the northern and southern sections of the river sections (Appendix 3.2.7a).

Future Outlook

Currently, the most numerically dominant species in the lower basin include anchovy, striped mullet, killifish, menhaden, Atlantic croaker, spot, silversides, and silver perch.

XI. Aquatic Life: Wetlands

Status and Trend: Unsatisfactory and Worsening

Description and Significance

Within the LSJRB, estuarine and freshwater wetlands functions to assimilate nutrients and pollutants from upland sources, minimize local flooding and run-off, shoreline stabilization, provide nursery grounds for fish and invertebrate species, refuge, nesting, and forage areas for resident and migratory birds; and critical habitat for a wide variety of aquatic and terrestrial wildlife.

Since the 1970s when wetlands were recognized as valuable resources, management efforts focused on how to compensate for the loss. Permit-seekers should first try to avoid wetlands; minimize impacts to wetlands, and compensate for the any losses. Compensation options include wetland enhancement, restoration, or creation. In addition, permit holders can opt to preserve wetlands and uplands. These efforts can occur on the property or in another location such as a designated conservation area. In addition, permit holders can mitigate impacts to wetlands by purchasing mitigation credits from a mitigation bank located in the same drainage basin. These mitigation banks are often located in rural areas and many miles from the location of the impacted wetland.

Ten Year Summary

Over the past ten years, the status of wetlands was UNSATISFACTORY. From 2008-2016, trends were UNCERTAIN and then changed to WORSENING in 2017. Within the past few years, environmental resource permit records have become more publicly accessible (SJRWMD 2016b), and therefore tracking of impacted wetland acreage and mitigation efforts is possible. With the end of the recession, a development boom has contributed to the number of wetlands lost to dredge and fill activities.

Future Outlook

Changes in land use, particularly the dredge and fill of wetlands for development contributes to overall loss in wetland acreage and function across the LSJR basin. In addition, rather than on-site mitigation with wetland creation or restoration, more permittees purchase mitigation credits from mitigation banks and/or preserve remaining wetlands. Because mitigation banks are typically miles from the impacted wetland, there is concern that the benefits that wetlands provide to ecosystems are shifting away from urban centers. Preservation of existing wetlands, although laudable, does not address the loss of wetlands due to dredge and fill activities.

XII. Aquatic Life: 3 Selected Threatened & Endangered Species

Status and Trend: Satisfactory and Improving or Stable

Wood Stork

Description and Significance

The wood stork (Mycteria americana) was listed as endangered in 1984 and is America’s only native stork. The reason for the Endangered Species Act (ESA) listing was declining numbers of nesting pairs from about 20,000 (1930s) to 3,000-5,000 pairs in the 1970s (Jacksonville Zoo 2017b).

Ten Year Summary

Originally recommended to be down listed (USFWS 2007d), wood stork was upgraded to Threatened status in June 2014 (USFWS 2017c). Over the past ten years, the status of the wood stork was SASTISFACTORY with a trend of IMPROVING. Data from a number of colonies in NE Florida, included Jacksonville Zoo and Gardens, Dee Dot ranch, Pumpkin Hill Creek Preserve State Park, and the Audubon winter bird count. According to Jacksonville winter bird counts by the Duval Audubon Society, numbers sighted have increased significantly from around 130 (2008) to 260 (2016), respectively. Historically, the wood stork breeding populations were located in the Everglades, but now their range has increased in extent and moved further north (Figure 10Yr-3). The birds continue to be protected under the Migratory Bird Treaty Act and state laws.

Figure 10Yr-3
Figure 10Yr-3. Wood stork nesting colonies (USFWS 2015).

Future Outlook

Threats continue to exist such as contamination by pesticides, harmful algae blooms, electrocution from power lines and road kills. Adverse weather events like severe droughts, thunderstorms, or hurricanes also threaten the wood storks The USFWS Wood Stork Habitat Management Guidelines help to address these threats. Continued monitoring is essential for this expanding and changing population (USFWS 2007d).

Bald Eagle

Description and Significance

The bald eagle (Haliaeetus leucocephalus) is a large raptor with a wingspan of about seven feet and represents a major recovery success story. Bald eagles were listed as endangered in most of the U.S. from 1967-1995 as a result of DDT pesticide contamination, which was determined to be responsible for causing their eggshells to be fragile and break prematurely. The use of DDT throughout the U.S. was subsequently banned, though it is still present in the environment (See Section 5.6 Pesticides). In 1995, bald eagle status was upgraded to threatened, and as a result of this tremendous recovery, bald eagles were delisted June 28, 2007 (USFWS 2007a; USFWS 2008a; USFWS 2008d; AEF 2016).

The eagles are found near large bodies of open water such as the St. Johns River, tributaries, and lakes, which provide food. Eagles feed on fish predominantly, but also eat birds, snakes, carrion, ducks, coots, muskrats, turtles, and rabbits. Nesting and roosting occurs at the tops of the highest trees (Scott 2003d; Jacksonville Zoo 2016; Jacksonville Zoo 2017a). Bald eagles are found in all of the United States, except Hawaii. Eagles from the northern United States and Canada migrate south to over winter while some southern bald eagles migrate north for a few months to avoid excessive summer heat (AEF 2017).

Ten Year Summary

Over the past ten years, the status of the Bald Eagle was SASTISFACTORY with a trend of IMPROVING. From 2006 to 2010, FWC data indicated that there was an average of 59 active nests out of a total of 107 bald eagle nests surveyed in the LSJRB. The nests were located mainly along the edges of the St. Johns River, from which the birds derive most of their food (Appendix 4.4.2.A.). Most of the nests seem to be in use about 57% of the time. When re-surveyed in 2013, the numbers of active nests had not changed significantly from 2010 (Figure 10Yr-4; Gipson 2014).

Figure 10Yr-4
Figure 10Yr-4. Bald eagle nesting sites in LSJRB 2013 (Gipson 2014).

Future Outlook

About 300-400 mated pairs nest every year in Florida and constitute approximately 86% of the entire southern population (Jacksonville Zoo 2017a). The primary law protecting bald eagles has shifted from the Endangered Species Act to the Bald and Golden Eagle Act (AEF 2014; USFWS 2008b; USFWS 2008c). According to the Duval Audubon Society who conduct winter bird counts in Jacksonville, numbers numbers sighted have increased significantly from around 15 (2008) to 40 (2016). Ongoing threats include harassment by people that injure and kill eagles with firearms, animal traps, power lines, windmills, poisons, contaminants, storms and habitat destruction, with the latter cause being the most significant (FWC 2008; USFWS 2008a; AEF 2017).

Florida Manatee

Description and Significance

In 1967, under a law that preceded the Endangered Species Act of 1973 the manatee was listed as an endangered species (Udall 1967). Manatees are also protected at the Federal level under the Marine Mammal Protection Act of 1972 (Congress 1972b), and by the State under the Florida Manatee Sanctuary Act of 1978 (FWC 1978). More recently, because manatees are no longer considered to be in imminent danger of extinction, the U.S. Fish and Wildlife Service announced that the West Indian manatee had been down-listed from Endangered to Threatened status on March 30, 2016. This action will not affect federal protections currently enforced under the ESA (USFWS 2016b; USFWS 2017b).

The Florida manatee (Trichechus manatus latirostris) is a large aquatic mammal that inhabits the waters of the St. Johns River year round and may reach a length of 12 ft and a weight of 3,000 lbs (Udall 1967; USFWS 2001).There are two sub-populations of manatees that use the LSJRB. The first sub-population consists of about 466 manatees from the Blue Springs area (Hartley 2016). Most of the animals in the LSJRB (about 260 manatees) (White and Pinto 2006b; White and Pinto 2006a) are members of the greater Atlantic region sub-population with 3,488 animals on the east coast, and 3,132 on the west coast of Florida, for a total of 6,620 manatees (FWRI 2017c).

Ten Year Summary

From 2008-2016, the status and trends of the Florida manatee has been SATISFACTORY and STABLE. In 2017, the trend was changed to IMPROVING. Prior to 2010, manatee mortality from watercraft was significantly high, responsible for 30% of total deaths. There appears to be a decreasing trend in watercraft-caused deaths for the LSJRB from 2010-2016, though if this trend is sustained or not remains unclear (FWRI 2017c). Speed zones have been in place for some time now, and improved education and outreach efforts coupled with increased law enforcement coordination has likely contributed in a positive way to the protection of manatees.

Future Outlook

Manatees in the LSJRB are likely to continue to increase as more manatees move north because of population increase throughout their southern range. Although multiple threats still exist, manatees do not appear to be in imminent danger of extinction. In 2013, the aerial survey budget was significantly reduced to the point that useful information about population trends is limited. The manatee count and distribution information in the form of maps is disseminated to local, state and federal law enforcement, maritime industry groups, the port, and the media so that efforts can be focused on raising public awareness through education. The focus on education is primarily so that manatee deaths from watercraft can be reduced.

On-going threats: Increased numbers of manatees and vessel traffic, salinity changes, sea level rise, and pollution loading

Although there is a decreasing trend in registered vessels in Duval and Putnam Counties, significant increases in vessel traffic in the LSJRB are projected over the next decade as the human population increases and commercial traffic doubles. More boats and more manatees could lead to more manatee deaths from watercraft because of an increased opportunity of boat encounters. Dredging, in order to accommodate larger ships, significantly affects boat traffic patterns and noise in the aquatic environment (Gerstein, et al. 2006) and has ecological effects on the environment that ultimately impact manatees and their habitat.

Freshwater withdrawals, in addition to harbor deepening, have likely contribute to the changes in salinity regimes in the LSJRB over time, but the size of the most recent impacts are predicted to be minimal based on the 2012 Water Supply Impact Study (SJRWMD 2012b). The study found that he maximum sustainable upstream surface water withdrawal and extent of impact to SAV in the LSJR was to be negligible relative to the normal inter-annual variation in the primary drivers of SAV colonization, water color and salinity intrusion, which in turn are driven by precipitation and runoff. If a sufficient change in salinity regimes occurs, it is likely to cause a die-off of the grass bed food resources for the manatee. This result would decrease carrying capacity of the environment’s ability to support manatees. As a result, the cumulative effects of freshwater withdrawals on these and other flora and fauna should be monitored to assess the impacts of water supply policy (NRC 2011).

Sea level rise is another factor likely to affect the SJR and requires detailed forecast modeling to determine potential impacts. In addition, any repositioning of point sources can alter pollution loading to the SJR and should be monitored for potential impacts to manatees (i.e., thermal/freshwater sources), as well as the grass beds on which they depend for food.

Important monitoring programs have been reduced or eliminated due to budget cuts in the last few years. Without consistent, detailed and current data, planners will be limited in their ability to gauge the effectiveness of programs that have the goal of improving environmental conditions in the river and may lead to additional costs in the future.

XIII. Aquatic Life: Non-native Aquatic Species

Status and Trend: Unsatisfactory and Worsening

Description and Significance

Non-native, or “exotic,” species are those that enter an ecosystem beyond its historic, native range, such as the cane toad, lionfish, Charua mussel, and water hyacinth. Common vectors of transport have been humans, ship ballast consisting of water and/or sediment, ship/boat hull fouling, and mariculture/aquaculture activities. In addition, people may accidentally or intentionally release exotic aquarium plants or pets into the wild. Such releases not only violate state and federal laws but also can have devastating impacts on native ecosystems and native biodiversity. Non-native flora and fauna can have few (if any) predators or pathogens in their new environment and thus have the potential to become invasive and out compete native organisms.  For example, the water hyacinth is the #1 aquatic weed in Florida because it chokes waterways and excludes native organisms.  Additionally, these non-native species can introduce microorganisms that can negatively impact human health. Removing or controlling these non-native species can be time-consuming and costly.

Ten Year Summary

Over the past ten years, the status of non-native aquatic species has been UNSATISFACTORY and the trend WORSENING. The estimated number of nonindigenous aquatic species was 56 in 2008 and increased to 80 in 2016. These species include submerged aquatic plants, molluscs, fish, crustaceans, amphibians, jellyfish, mammals, reptiles, and algae. For example, the spread Cuban treefrog and lionfish is of increasing concern.

Future Outlook

Educational outreach that emphasizes the economic, social, and environmental impacts of invasive species can help deter future invasions. For example, citizen scientist programs that enable the public to quickly and easily report species locations with online tracking sites can be used to help resource managers eradicate newly invading species.