4. Aquatic Life

4.1. Submerged Aquatic Vegetation (SAV)

4.1.1. Description

Dating back to 1773, records indicate that extensive SAV beds existed in the river (Bartram 1928). Since that time, people have altered the natural system by dredging, constructing seawalls, contributing chemical contamination, and sediment and nutrient loading (DeMort 1990; Dobberfuhl 2007). SAV found in the LSJRB (see Table 4.1) 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. Water naiad and widgeon grass form bands within the shallow section of the SAV bed. Tape grass is a freshwater species that tolerates brackish conditions, water naiad is exclusively freshwater and wigeon grass is a brackish water species that can live in very salty water (White, et al. 2002; Sagan 2010). Ruppia does not form extensive beds. It is restricted to the shallow, near shore section of the bed and has never formed meadows as extensive as Vallisneria even when salinity has eliminated Vallisneria and any competition, or other factors change sufficiently to support Ruppia (Sagan 2010).

Other freshwater species include: muskgrass (Chara sp.), spikerush (Eleocharis sp.), water thyme (Hydrilla verticillata; an invasive non-native weed), baby’s-tears (Micranthemum sp.), sago pondweed (Potamogeton pectinatus), small pondweed (Potamogeton pusillus), awl-leaf arrowhead (Sagittaria subulata) and horned pondweed (Zannichellia palustris) (IFAS 2007; Sagan 2006; USDA 2013). DeMort 1990 surveyed four locations for submerged macrophytes in the LSJR and indicated that greater consistency in species distributions occurred south of Hallows Cove (St. Johns County) with tape grass being the dominant species. North of this location, widgeon grass and sago pondweed were the dominant species until 1982-1987, when tape grass coverage increased 30%, and is now the most dominant species encountered.

The greatest distribution of SAV in Duval County is in waters south of the Fuller Warren Bridge (Kinnaird 1983b; Dobberfuhl 2002; Dobberfuhl and Trahan 2003; Sagan 2004; Sagan 2006; Sagan 2007). 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. Dobberfuhl 2007 confirmed that the deeper outer edge of the grass beds occurs at about three feet in the LSJRB. Rapid regeneration of grass beds occurs annually in late winter and spring when water temperatures become more favorable for plant growth and the growing season continues through September (Dobberfuhl 2007; Thayer, et al. 1984). SAV beds, especially Vallisneria, are present year-round and are considered “evergreen” in Florida (Sagan 2010).

Sunlight is vital for good growth of submerged grasses. Sunlight penetration may be reduced because of increased color, turbidity, pollution from upland development, and/or disturbance of soils. Deteriorating water quality has been shown to cause a reduction in grass beds. This leads to erosion and further deterioration of water quality.

In addition to the amount of light, the frequency and duration of elevated salinity events in the river can adversely affect the health of SAV (Jacoby 2011). In lab studies, Twilley and Barko 1990 showed that tape grass grows well from 0-12 parts per thousand of salinity and can tolerate water with salinities up to 15-20 parts per thousand for short periods of time. Also, SAV requires more light in a higher salinity environment because of increased metabolic demands (Dobberfuhl 2007). Finally, evidence suggests that greater light availability can lessen the impact of high salinity effects on SAV growth (French and Moore 2003; Kraemer, et al. 1999).

Dobberfuhl 2007 noted that, during drought conditions, there is an increase in light availability that likely causes specific competition between the grasses and organisms growing on the surface of the grasses (Table 4.1). Many of these epiphytic organisms block light and can be detrimental to normal growth of the tape grass. As a result, this fouling causes an increase in light requirements for the SAV (Dunn, et al. 2008).

Table 4.1 Submerged aquatic vegetation in the Lower St. Johns River.

Table 4.1.1
(Photo: SJRWMD)
Tape grass (Vallisneria americana)
• Teeth on edge of leaves
• Leaves flat, tape-like; 0.5-4 cm wide
• Leaves taper at tip
• No obvious stem
• Height: 4-90 cm
(a small one can be confused with Sagittaria subulata)
(Photo: SJRWMD)
Water naiad (Najas guadalupensis)
• Leaf whorls not tightly packed
• Leaf pairs/whorls separated by large spaces on stem
• Leaves opposite, usually in pairs, sometimes in whorls of three
• Leave with teeth (must look closely); 2 mm wide
Table 4.1.3
(Photo: SJRWMD)
Widgeon grass (Ruppia maritima)
• Leaves alternate, tapering at end
• Leaves thread-like; 0.5 mm wide
• Height: 4-20 cm
Table 4.1.4
(Photo: Kerry Dressler)
Muskgrass (Chara sp.)
• Leaf whorls separated by conspicuous spaces
• Leaf not forked
• Leaves stiff and scratchy to touch
• Height: 2-8 cm
(Photo: SJRWMD)
Spikerush (Eleocharis sp.)
• No teeth on leaves
• Leaves round, pencil-like; 1-3 mm wide
• Leaves as broad at tip as at base
• Height: 1-5 cm
(Photo: Kerry Dressler)
Water thyme (Hydrilla verticillata)
• Leaf whorls tightly packed
• Leaves opposite, in whorls of four to eight leaves
• Leaves with conspicuous teeth, making plant scratchy to the touch
• Leaf tip pointed; leaves 2-4 mm wide
• Height: 5-15 cm
Table 4.1.7
(Photo: SJRWMD)
Baby’s-tears (Micranthemum sp.)
• Leaf whorls not tightly packed
• Leaf opposite, in whorls of three to four leaves
• No teeth on leaves
• Leaf tip rounded; 2-4 mm wide
• Height: 2-15 cm
Table 4.1.8
(Photo: SJRWMD)
Sago pondweed (Potamogeton pectinatus)
• Leaves alternate; 0.5-4.5 cm wide
• No teeth on leaves
• Leaves long and narrowing with pointed tips
• Stems thread-like
• Height: 5-20 cm
Table 4.1.9
(Photo: SJRWMD)
Small pondweed (Potamogeton pusillus)
• Leaves alternate; 0.5-3 mm wide
• No teeth on leaves
• Leaves long and narrow with blunted or rounded tips
• Stems thread-like
• Height: 5-20 cm
(Photo: SJRWMD)
Awl-leaf arrowhead (Sagittaria subulata)
• No teeth on leaves
• Leaves triangular, spongy; 3-8 mm wide
• Leaves taper at tip
• Height: 1-5 cm
Table 4.1.11
(Photo: SJRWMD)
Horned pondweed (Zannichellia palustris)
• Leaves opposite
• No teeth on leaves
• Long narrow leaves with blunted tips
• Stems thread-like
• Often seen with kidney-shaped fruit
• Height: 1-8 cm

4.1.2. Significance

SAV provides nurseries for a variety of aquatic life, helps to prevent erosion, and reduces turbidity by trapping sediment. Scientists use SAV distribution and abundance as major indicators of ecosystem health (Dennison, et al. 1993). 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 (White, et al. 2002). Manatees consume from 4-11% of their body weight daily, with Vallisneria americana being a preferred food type (Bengtson 1981; Best 1981; Burns Jr, et al. 1997; Lomolino 1977). Fish and insects forage and avoid predation within the cover of the grass beds (Batzer and Wissinger 1996; Jordan, et al. 1996). 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.

Over the years, dredging to deepen the channel for commercial and naval shipping in Jacksonville, has led to salt water intrusion upstream. The magnitude of this intrusion over time has not been well quantified (See Section 1.2.3 Ecological Zones). Further deepening is likely to impact salinity regimes that could be detrimental to the grass beds. This is especially important if harbor deepening were to occur in conjunction with freshwater withdrawals for the river (SJRWMD 2012a). On April 13, 2009, the Governing Board of the SJRWMD voted on a permit to allow Seminole County to withdraw an average of 5.5 million gallons of water a day (mgd) from the St. Johns River. Seminole County’s Yankee Lake facility would eventually be able to withdraw up to 55 mgd. This initial permit from Seminole County represents the beginning of an Alternative Water Supply (AWS) program that would result in the withdrawal of water from the St. Johns and Ocklawaha Rivers (St. Johns Riverkeeper 2009). The impact of water withdrawal on salinity was investigated by a team of researchers from the SJRWMD, and the final recommended sustainable withdrawal from the Water Supply Impact Study was 155 MGD. The National Research Council peer review committee provided peer review, and the final report was made available in early 2012 (NRC 2012).

4.1.3. Data Sources & Limitations

The SJRWMD conducted year-round sampling of SAV from 1998 to 2011 at numerous stations (about 152 stations along line transects of 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 2015/2016 to include fewer stations than before (Jacksonville to Black Creek/Hallows Cove, about 40 stations). This type of field sampling provides information about inter-annual relative changes in SAV by site and region. Data evaluated in this report is for the years 1989, 2000 through 2011, and 2000 through 2015 for the latest limited sampling program in the northern section. For maps of the individual transect locations, see Appendix

The parameters used as indicators of grass bed condition were (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. The data were broken down into six sections of the St. Johns River as follows: (1) Fuller Warren to Buckman, (2) Buckman to Hallows Cove, (3) Hallows Cove to Federal Point, (4) Federal Point to Palatka, (5) Palatka to Mud Creek Cove, and (6) Crescent Lake (Appendix The most recent data for (1) Fuller Warren to Buckman Bridge and (2) Buckman Bridge to Hallows Cover sections have been updated in this report. The data set includes a couple of the most intense El Niño years (1998, and 2015) the former, followed by one of the most intense drought periods (1999-2001) in Florida history. Both of these weather phenomena exaggerate the normal seasonal cycle of water input/output into the river. Also, a series of shorter droughts occurred during 2005-2006 and 2009-2010. Normally, grass bed length on western shorelines tends to be longer than on eastern shorelines; and this is likely because of less wave action caused by the prevailing winds and broader shallower littoral edges compared to the east bank. Therefore, the shore-to-shore differences are most pronounced in Clay County-western shore sites and St. Johns County-eastern shore sites (Dobberfuhl 2009). For a list of grass species encountered within each section and a comparison of the variation among grass bed parameters, including canopy height and water depth, see Appendix A-D.

Because of the importance of color and salinity, rainfall and salinity levels were examined. Rainfall data were provided by SJRWMD (Rao, et al. 1989; SJRWMD 2017) (Figure 4.1), the National Hurricane Center (NOAA 2017a), and the Climate Prediction Center (NOAA 2013) (see Appendix for Rainfall, Hurricanes, and El Niño). Salinity data from 1991 to 2015 were provided by the Environmental Quality Division of the COJ. Water quality parameters are measured monthly at ten stations in the mainstem of the St. Johns River at the bottom (5 m), middle (3 m), and surface (0.5 m) depths. Additional data on salinity from 1994 to 2011 came from the SJRWMD, and correspond with five specific SAV monitoring sites (Appendix Salinity). These data are discussed further in Section 4.4 Threatened & Endangered Species. Note that “spot sampling” cannot be used to adequately match water quality parameters and grass bed parameters; because plants like Vallisneria integrate conditions that drive their responses. To evaluate such responses, “high-frequency” data are required (Jacoby 2011). Moreover, information is limited about duration and frequency of elevated salinity events in the river and how that relates to the frequency and duration of rainfall. Also, there is limited information about the ability of SAV growing in different regions of the river to tolerate varying degrees of salinity. In 2009, the SJRWMD began to conduct research to evaluate this question by transplanting tape grass from one area to other areas in the river, thus exposing it to varying degrees of salinity for varying periods of time (Jacoby 2011). These same concerns are echoed by the Water Science and Technology Board’s review of the St. Johns River Water Supply Impact Study (NRC 2011, p. 5) – see a list of select findings under Section 4.1.5. Future Outlook.

4.1.4. Current Status & Trend

The status and trend was based on the significance of evaluated grass bed parameters using Kendall’s Tau correlation analysis. For the period 1989, and 2000 through 2007, the section of the St. Johns River north of Palatka had varying trends in all the parameters that usually increase and decrease according to the prevailing environmental conditions. For the period 2001-2011, the data showed a declining trend in grass bed parameters – this is in spite of some recovery in grass beds condition in 2011. Also, salinity was negatively correlated with percent total cover and the proportional percent of tape grass (Appendix The degree to which this occurred was greater north of the Buckman Bridge compared to south of the bridge.

North of the Buckman Bridge: the average grass bed length declined from 139 m (1998) to 22 m (2011). Surveys were suspended due to budget cuts from 2012 to 2014. When sampling was resumed in the area during 2015/16, the average grass bed length was to 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 the north 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. Surveys were suspended due to budget cuts from 2012 to 2014. When sampling was resumed in the area 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.

Although still below 1998 levels, the 2015 and 2016 data from SJRWMD indicate that grass beds in the northern section of St. Johns River have regrown significantly compared to 2011 levels. This is likely due to fresher conditions from 2012 to 2015 when more normalized and stable rainfall conditions prevailed (Figure 4.1). However, it is important to note that this represents just two years of data, and more years of data are required to see if the trend is sustained particularly coming out of the current El Niño season (2015) and entering into another severe period of drought affecting the whole State of Florida. The grass beds from the Buckman Bridge to Hallows Cove do not appear to have undergone significant changes since 2011.

There was a declining trend in all the parameters (2001-2007) south of Palatka and in Crescent Lake. From 2007-2009 the data suggested an increasing trend in all parameters. In 2010, data showed a declining trend, but in 2011 the trend was increasing again. However, over the longer-term (2001-2011) there was a declining trend in grass bed length (Appendix There was no new data for these areas of the river in 2015/2016.

The availability of tape grass decreased significantly in the LSJRB during 2000-2001. This may be because the severe drought during this time caused higher than usual salinity values which contributed to high mortality of grasses. Factors that can adversely affect the grasses include excess turbidity, nutrients, and phytoplankton (see Section 2.5 Algae Blooms). In 2003, environmental conditions returned to a more normal rainfall pattern. As a result, lower salinity values favored tape grass growth. In 2004, salinities were initially higher than in 2003 but decreased significantly after August with the arrival of heavy rainfall associated with four hurricanes that skirted Florida (Hurricanes Charley, Francis, Ivan and Jeanne). Grass beds north of the Buckman Bridge regenerated from 2002-2006 and then declined again in 2007 due to the onset of renewed drought conditions (White and Pinto 2006b). Drought conditions ensued from 2009-2010, leading to a further decline in the grass beds. From 2012-2015, rainfall has been near average and stable, favoring grass bed growth again in the northern sections of the river. Under normal conditions, SAV in the river south of Palatka and Crescent Lake is dynamic (highly variable) and significantly influenced by rainfall, runoff, and water color (Dobberfuhl 2009). Taking everything into account, and particularly because of limited data and coverage, the current STATUS of SAV is unsatisfactory, and the TREND is uncertain.

Figure 4.1
Figure 4.1 Monthly rainfall maximum, minimum, long term and short term annual means for LSJRB. Data are for the period June 1995 to December 2015 (solid lines). Average of monthly rainfall for periods 1951-1960 and 1995-2015 were not significantly different (dotted line) (Data source: SJRWMD 2016a).

4.1.5. 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 and their livelihood. Further indices of the health and status of grass beds should be developed that express the economic value of the resource as it pertains to habitat ecosystem services, fisheries and other quality-of-life indices such as aesthetics, recreation, and public health. 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.

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 the 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 2012).

Select findings of the St. Johns River Water Supply Impact Study: Final Report (NRC 2012):

  • “the workgroups did not appear to consider the possibility of “back-to-back extreme events in their analyses, e.g., two or three years of extreme drought in a row, which the Committee considers to be reasonably likely future situations.” p. 97
  • “they also tended to present mean responses to perturbations of a given driver with little or no consideration of the variance in that response. Although mean values are considered the most likely responses from a statistical perspective, in analyzing potential environmental impacts of changes in driver variables it is important to consider ranges (or variances) of responses. Although such responses may be less likely than mean values, they may not have negligible probabilities and they also could be much more detrimental than the mean responses. The Committee remains concerned that the District did not consider such conditions sufficiently in their otherwise thorough analyses.” p. 97
  • “Several critical issues that are beyond the control of the District or were considered to be outside the boundaries of the WSIS limit the robustness of the conclusions. These issues include future sea-level rises and increased stormwater runoff and changes in surface water quality engendered by future population growth and land-use changes. As discussed in Chapter 2, the predicted effects of some of these issues on water levels and flows in the river are greater in magnitude than the effects of the proposed surface water withdrawals, but they have high uncertainties. In addition, the relatively short period (ten years) of the rainfall record used for the hydraulic and hydrodynamic modeling and the assumption that it will apply to future climatic conditions is a concern. The Committee recognizes that changing climatic conditions globally are rendering long-term historic records less and less useful in making extrapolations to future rainfall patterns, particularly for time periods in the more distant future (e.g., 25-50 years from now). The District should acknowledge this limitation in its final report and should plan to run its models with more recent rainfall records in an adaptive management mode.” p. 100-101
  • “The Committee continues to be somewhat concerned with the basis for the final conclusion that water withdrawals of the magnitude considered in the WSIS will not have many deleterious ecological effects. In large part, this conclusion was based on the model findings that increased flows from the upper basin projects and from changes in land use (increases in impervious urban/suburban areas) largely compensated for the impacts of water withdrawals on water flows and levels. Although the upper basin projects should be viewed as a positive influence insofar as they will return land to the basin (and water to the river) that belonged there under natural conditions, the same cannot be said about increased surface runoff from impervious urban- and suburbanization. The generally poor quality of surface runoff from such land uses is well known. Uncertainties about future conditions over which the District has no control (e.g., climate change, sea level rise, land use) also lead to concerns about the reliability of the conclusions.” p. 100-101
  • “the WSIS should have included a water quality workgroup that addressed the effects of changing land use on runoff and return flow water quality throughout the basin. It is clear that future needs for additional water supplies in the St. Johns River basin will be driven by population increases that also will result in land-use changes—essentially increases in urban/suburban land cover—and increases in the production of wastewater effluent. Both of these changes are highly likely to affect surface water quality in the basin. The District argued that these considerations were beyond their scope and authority and that existing regulations such as NPDES permits and stormwater regulations would be sufficient to prevent water quality degradation. Although the Committee accepts the District’s argument that it lacks authority to control land use and population growth, it does not accept the view that this means the District has no responsibility to consider these issues in a study on the environmental impacts of surface water withdrawals.” p. 104
  • “District scientists found that the lack of basic data (e.g., certain kinds of benthos and fish information) and the inadequacy of basic analytical tools (e.g., on wetland hydrology and biogeochemical processes) limited what they were able to achieve and conclude. Some of these deficiencies could be overcome by future work of District scientists, and these needs should be addressed in the District’s medium- and long-term planning for future studies.” p. 104