2.8. Salinity

2.8.1. Overview

Salinity is a measure of the amount of salt that is dissolved in a sample of water. It is measured in parts per thousand (ppt), or practical salinity units (psu), or it can be calculated from measuring the electrical conductivity of a water sample.  On average, salinity ranges from about 35 parts per thousand at the ocean (full strength seawater) to about 10-18 ppt near downtown Jacksonville (brackish water), and 0-5 ppt near the Buckman Bridge (fresh water). However, depending on the offshore water levels, tide (moon phase), flow, winds locally and offshore (Bacopoulos et al. 2009), and weather, the salinity in the river can vary considerably at a given time and place from 1-2 day spikes to an extended duration of weeks and months.  The salty waters are diluted by freshwater that enters the river primarily from precipitation (mostly June-October) and springs or other aquifer/groundwater connections. The amount of flow from springs can be significantly reduced during droughts, because the groundwater level that feeds the spring may decrease (CFWI 2015; Beck 2018). Salinity increases during periods of droughts, and the effects can be exacerbated if they are more frequent such as in back to back years.  In addition, there are springs with high salinity that affect localized areas within the St. Johns River. For example, the input from Salt Spring (Marion County) causes elevated salinity (>5 ppt) in otherwise freshwater sections of the river because of high salts and calcium content (Benke and Cushing 2005).

The St. Johns River estuary also experiences significant tidal forcing which affects the salinity depending on the discharge rates at the river mouth which ranges from 2-8 billion gallons per day (Miller 1998). If tidal exchange is included, flow at the mouth can increase to about 14 billion gallons per day (Sucsy 2008). During Hurricane Irma (September 2017), the river’s discharge increased to about 88 billion gallons per day (Mundy 2018) due to increased rainfall and the river turned fresh for several months near downtown Jacksonville. Fishing and shrimping was significantly reduced as salt water species were likely forced to move closer to the ocean. However, at times, the St. Johns River flows backwards up to 160 miles for several weeks, as far as Lake Monroe (Durako et al. 1988). The main reason for these reversed flows is the river’s slow movement and flat bottom with a mild gradient that averages about 2.2 cm/km (Toth 1993), while the tidal range at Mayport is comparatively larger at about 2 m (McCully 2006). Flooding is common when wind from storms creates a surge of water traveling upstream, and then later also downstream, as with Hurricane Irma (Aug-Sept 2017). This is important because salinity variations can have far-reaching effects on the ecology of the river. The flow of freshwater into an estuary, its timing and delivery, are crucial to biological productivity (Cross and Williams 1981). The adverse effects of reducing freshwater flowing into Apalachicola Bay, which has decimated the ability to harvest oysters, have demonstrated this (Livingston 2008; Montagna et al. 2011).

Figure 2.58 Map of the Ecological (Salinity) Zones of the Lower St. Johns River (Source: Hendrickson and Konwinski 1998; Malecki et al. 2004).
Figure 2.58 Map of the Ecological (Salinity) Zones of the Lower St. Johns River (Source: Hendrickson and Konwinski 1998; Malecki et al. 2004).

Interestingly, the lowest salinity occurs in the area from Green Cove south to Palatka, but then it tends to increase again because ground water entering the river has high salts and calcium content (Benke and Cushing 2005).

Mulamba et al. 2019 indicate that increasing salinity effects are likely to be felt throughout the whole estuary regardless of the magnitude of sea-level rise. Modeling of sea-level rise for three scenarios indicated that linear rates of salinity increase were predicted as high as 6 ppt m−1 inside the river. The change in salinity was non-uniform throughout the system, because the river geometry changes, becoming shallower south of downtown Jacksonville (20 Km from the river mouth). The model results indicated a hotspot in the river where salinity was predicted to increase by about 2 ppt (near river Km 30, or in-between the Acosta Bridge and Buckman Bridge (40 Km from the river mouth).

2.8.2. Biological Impacts

This sub-section covers potential biological impacts of salinity on the flora and fauna of LSJRB (Mulamba et al. 2019). Salinity increases as a result of the environment can be looked at in terms of: 1) periodic short term events like storms that result in abrupt salinity spikes for less than 14 days; 2) Intermediate term events like droughts that result in elevated salinity for some weeks; 3) Long-term changes as a result of sea levels rising over many years; and 4) Human activities in the basin, such as reduced freshwater inflows to the river caused by dams, surface water withdrawals, or significant pumping of ground water. In addition, activities, such as harbor deepening, tend to increase salt water entering an estuary, thus driving up the salinity (Sucsy 2008).

The LSJRB supports a diverse community of living organisms that are important to the ecosystem, are affected by salinity, and have significant recreational and commercial economic value. Submerged aquatic vegetation and invertebrate bottom dwelling organisms play an important role in shaping habitat so that it is able to support fish and other wildlife. Examples of commercially valuable organisms include blue crabs, bait shrimp, and stone crabs. In 2017, Clay, Duval, Flagler, Putnam, and St. Johns Counties reported a total commercial crab harvest of 1,495, 787 lbs (82%); and a fish harvest of some 278, 130 lb (FWRI 2019a). In general, striped mullet, whiting, and flounder have been the most caught species, but recreationally, red drum, spotted sea trout, croaker, sheepshead, flounder, largemouth bass, and blue gill are most important to anglers.

For all the species of fish and invertebrates mentioned in this report there are a few themes of importance:

  • Each species plays an essential role in the ecosystem, with many interdependencies (predator, prey relationships).
  • Each species requires essential habitats for an important life stage (coastal and in the river).
  • Each species is of commercial and recreational value that is supported by the rest of the ecosystem, which also has value.

The most recent Supplemental Environmental Impact Statement (SEIS) by the USACE regarding dredging in the St. Johns River indicated that salinity changes, as a result of dredging, would negatively impact the distribution of Submerged Aquatic Vegetation (SAV) in LSJR. The impact would likely be from increased salinity stress on SAVs in the most northern part of their range in LSJR (Duval, Clay, and St. Johns Counties). Moreover, the report states that the 46 feet and 50 feet dredge depth scenarios would increase salinity stress by 32 and 43 acres of potential SAV habitat per day, respectively. This would most likely lead to a reduction in manatee forage habitat, essential fish habitat, benthic macro-invertebrate habitat and freshwater wetlands (USACE 2014a). In addition, the report states that loss of SAVs would represent a small portion of the total available SAVs in the LSJR, also that blue crabs and other marine species may benefit from any increases in salinity. In Appendix E of the report (USACE 2014b), the USACE pledged to monitor salinity and water quality to ensure appropriate mitigation. Furthermore, that the mitigation for SAVs lost is to be accomplished through a Corrective Action Plan that would purchase conservation lands (638 acres of freshwater wetlands, uplands, river shoreline, and saltmarshes).

In the report, the USACE states that the analysis and conclusions were based on modeling efforts that make certain assumptions about the rate of sea level rise (hydrodynamic modeling), and that salinity stress on SAVs was developed from a separate modeling analysis (Taylor 2013a) based on assumptions about levels of salinity stress and SAV acreages (ecological modeling). The hydrodynamic model reports (Taylor 2011; Taylor 2013b; Taylor 2013c) presented error statistics for the EFDC and CE-QUAL-ICM models. However, similar error statistics could not be calculated for the ecological models, and that represents an uncertain risk associated with evaluation of the ecological model results. Moreover, the report stated that, “Future condition hydrodynamic model simulations further rely on assumptions about the rate of sea level rise, quantity of water withdrawal from the middle St. Johns River, patterns of land use, and other factors. Actual conditions will deviate from those used to drive the models. These deviations introduce additional uncertainty in the models’ ability to predict future conditions and impacts. These uncertainties are; however, inherent in the use of numerical models and do not represent an unknown risk” (USACE 2014a; Section 7.2, p. 258).

On February 19, 2016, the DEP issued a Notice of Intent to issue an Environmental Resource Permit and a Variance to allow the Army Corps of Engineers to dredge 13 miles of the St. Johns River from the mouth of the river to Brills Cut from a depth of 40 feet to up to 51 feet. The St. John RIVERKEEPER filed a Petition for Formal Administrative Hearing against DEP on April 1, 2016, based on the contention that the potential environmental impacts were not adequately addressed in the permit and important water quality standards are waived increasing the inherent risks of the proposed deep dredge. The USACE reacted by filing a Notice of Non-Participation asserting sovereign immunity and indicating that it does not plan to participate as a party in the administrative proceeding. This is an unprecedented move, which is likely to create the potential for more risk since the USACE contends that they are immune from abiding to Florida water quality standards. On July 26, 2016 St. Johns RIVERKEEPER filed a notice withdrawing its legal challenge of the state permit due the lack of enforceability with the intent to elevate the challenge to the federal level. On Friday, April 7, 2017, St. Johns RIVERKEEPER filed a Complaint for Declaratory and Injunctive Relief in federal court against the USACE regarding the proposed St. Johns River harbor deepening project. The injunction was not upheld by the court (December 2017), and so while the legal challenge continues at the federal level, in February 2018 the USACE began to dredge an initial 3-mile section of the main St. Johns River channel near Mayport. Macroinvertebrates

These are animals without a backbone that live in or on river bottom sediments including small crabs, snails, shrimp, clams, insects, worms, and barnacles among others species (see Section 4.3). These organisms affect oxygen levels in the sediment, as well as sediment size, which in turn affect what is able to live and grow in proximity to them.  Macroinvertebrates are useful indicators of environmental stress and species change as one transitions from higher to low salinity. DEP data from 1974-1999 indicated that the northern river section was dominated by barnacles, polychaetes, and amphipods; and the southern river area was dominated by mollusks, amphipods, polychaetes, oligochaetes, and fly larvae. During the 1980s, the north section was dominated by polychaetes and barnacles, while the southern portion was mostly oligochaetes and fly larvae. In the 1990s, another shift occurred due to salinity, where the northern stations were dominated by amphipods, mollusks, polychaetes, and barnacles and the southern areas by bivalves and snails (Evans et al. 2004; Montagna et al. 2011).

Evans et al. 2004 states that freshwater areas of the river are affected by increasing salinity and that the concern is this will likely change the invertebrate community, the result could be significant negative impacts on the quality and quantity of freshwater fish species harvested from LSJRB. At this time, there is a lack of recent data on macroinvertebrates and how parameters, such as low dissolved oxygen, sediment quality, and toxic substances in the environment, may interact with changes in salinity levels. Blue Crabs

The blue crab is a common benthic predator that represents the largest commercial fishery in LSJRB. Successful crab reproduction relies on a particular set of salinity conditions at specific times in the life cycle. Females carry fertilized eggs and migrate towards the more marine waters near the mouth of the river where they will release their eggs into the water (see section 3.3.2 Fisheries). After some time adrift, wind and currents transport the megalops larvae back to the estuarine parts of the river where they settle in submerged aquatic vegetation (SAV) that serves as a nursery.

One concern that may negatively affect the recruitment of new crabs into the population is that with increasing salinity levels, the salinity transition zone will shift further south increasing the distance that female crabs with eggs will need to travel in order to reach the river mouth. This could ultimately affect recruitment.

Another concern is associated with nursery habitat. Increasing salinity further south in the river will negatively impact submerged aquatic vegetation that is required for young crabs.

Also, since the price of crustaceans in general is dependent on size, yet another concern may be diminishing size of adult crabs. There are several studies mentioned in Tagatz 1968a that report an inverse relationship between salinity and size. The higher the salinity of water in which growth occurs the smaller the adult sizes. This may be due to the crabs absorbing more water in lower salinity conditions when they molt (bigger crab) as opposed to them absorbing less water under higher salinity conditions (smaller crab). As a result, this could translate into lower income per pound for commercial harvesters for a particular level of fishing effort.

Ecologically speaking, 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 (White et al. 2009). Shrimp

Three principle shrimp species found in the area include most commonly White Shrimp (Litopenaeus setiferus), Brown Shrimp (Farfantepenaeus aztecus), and Pink Shrimp (Farfantepenaeus duorarum). All are omnivores feeding on worms, amphipods, mollusks, copepods, isopods and organic detritus. White shrimp spawn from April to October; pink shrimp (February to March) and brown shrimp (March to September) (FWRI 2008d). All species spawn offshore in deeper waters with larvae developing in the plankton and eventually settling in salt marsh tidal creeks with appropriate salinities within the estuaries. Changes in salinity will cause a change in the distribution of these early life stages that could potentially affect the number of adults returning offshore. Shrimp are important in both benthic and planktonic food webs in SJR. They affect the abundance of many small macroinvertebrates. They are also important prey for many other species. As small planktonic individuals, the shrimp post‐larvae and juvenile forms provide food for other estuarine species like sheepshead minnows, insect larvae, killifish, and blue crabs. As adult shrimp, they are preyed on by finfish found within the river. The commercial shrimp fishery is one of the largest fisheries in the region, but most shrimp for human consumption are caught offshore. Fish

The SJRWMD (McCloud 2010) compared current FWRI fish data with those collected by Tagatz in 1968 (Tagatz 1968b). The data suggested that at some areas of the river, fish communities were 50% different between 1968 and the 2001-2006 time periods. The differences in fish communities in these areas may have been the result of a transition zone between marine and freshwater moving further upstream (Figures 2.58-2.60). It is important to note that most fish are able to move from an area in response to changes in environmental factors, such as salinity, dissolved oxygen, and temperature. However, sessile species of plants and animals that are closely associated with the bottom substrate cannot move and can be impacted by such variations depending on the frequency and duration of events. Moreover, for the species that can move, there may be important life stages for these that dependent on water quality parameters being relatively stable at essential habitat areas like nursery and spawning grounds. Although fish can move, they may not be able to reproduce effectively because essential habitat has been disrupted that affects a particular life stage.

Figure 2.59 Salinity on the bottom of SJR (Station SJR17 near JU) values above the bars indicate the numbers of observations. Solid line (mean), vertical lines (maximum and minimum), and bars (Standard Deviation of the mean) (Data source: Karlavige 2019). SJR17 mean 25.03‰ (SD ± 5.07) for the maxima. Note that only 5 observations were made in 2013; 4 in 2014, 3 in 2016, and 4 in 2018.
Figure 2.59 Salinity on the bottom of SJR (Station SJR17 near JU) values above the bars indicate the numbers of observations. Solid line (mean), vertical lines (maximum and minimum), and bars (Standard Deviation of the mean) (Data source: Karlavige 2019). SJR17 mean 25.03‰ (SD ± 5.07) for the maxima. Note that only 5 observations were made in 2013; 4 in 2014, 3 in 2016, and 4 in 2018.


Figure 2.60 Salinity on the bottom of SJR (Mainstem Station SJR40 located mid-channel N. of Piney Pt. 100 m west of green marker 5) values above the bars indicate the numbers of observations. Solid line (mean), vertical lines (maximum and minimum), and bars (Standard Deviation of the mean) (Data source: Karlavige 2019). SJR40 mean 13.67‰ (S.D. ± 5.50 for the maxima). Note that only 5 observations were made in 2013; 2 in 2014, 3 in 2016, and 4 in 2018.
Figure 2.60 Salinity on the bottom of SJR (Mainstem Station SJR40 located mid-channel N. of Piney Pt. 100 m west of green marker 5) values above the bars indicate the numbers of observations. Solid line (mean), vertical lines (maximum and minimum), and bars (Standard Deviation of the mean) (Data source: Karlavige 2019). SJR40 mean 13.67‰ (S.D. ± 5.50 for the maxima). Note that only 5 observations were made in 2013; 2 in 2014, 3 in 2016, and 4 in 2018.


Figure 2.61 Salinity on the bottom of SJR (Station SJR34/34A located ~ 1000 m south of Doctors Lake on the west bank) values above the bars indicate the numbers of observations. Solid line (mean), vertical lines (maximum and minimum), and bars (Standard Deviation of the mean). (Data source: Karlavige 2019). SJR34/34A mean 7.76‰ (SD ± 4.51) for the maxima. Note that only 5 observations were made in 2013, 1 in 2014, 3 in 2016, and 5 in 2018.
Figure 2.61 Salinity on the bottom of SJR (Station SJR34/34A located ~ 1000 m south of Doctors Lake on the west bank) values above the bars indicate the numbers of observations. Solid line (mean), vertical lines (maximum and minimum), and bars (Standard Deviation of the mean). (Data source: Karlavige 2019). SJR34/34A mean 7.76‰ (SD ± 4.51) for the maxima. Note that only 5 observations were made in 2013, 1 in 2014, 3 in 2016, and 5 in 2018.

With regard to living organisms, changes in water quality parameter averages are not as meaningful as the changes that may occur in the parameter extremes – like salinity maxima and dissolved oxygen minima. If any changes were to persist for an extended time or if they occurred too abruptly then this is likely to be detrimental to survival. Salinity changes may potentially affect the distribution of these fish within estuary creeks and the river by affecting prey distributions for different life stages. As the salinity zone shifts further south, fresh water species are likely to be more impacted than more salt tolerant species.

Red Drum (Sciaenops ocellatus): Red drum is predatory fish that are found in the SJR estuary. The juveniles move into estuary creeks and rivers. Red drum is ecologically in the food web of the St. Johns River where 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; however, drum has not been commercially harvested since 1988.

Spotted Seatrout (Cynoscion nebulosus): The spotted seatrout is another bottom-dwelling predator common to estuaries and shallow coastal habitats. It feeds on small fish species such as anchovies, pinfish and menhaden as well as shrimp. Spotted seatrout larvae feed mostly on copepods, which are part of the plankton. There are a number of predators that feed on seatrout including Atlantic croakers, cormorants, brown pelicans, bottlenose dolphins, and sharks. These fish have significant commercial and recreational value.

Largemouth Bass (Micropterus salmoides): Largemouth bass are predators in brackish to freshwater habitats in SJR, including lakes and ponds. The young feed on zooplankton, insects and crustaceans including crayfish. Adults feed on a variety of larger fish, crayfish, crabs, frogs, and salamanders. Spawning occurs from December to May, with males constructing nests and guarding young in hard-bottom areas near shorelines. Largemouth bass are aggressive predators, significantly affecting the abundance of many organisms in the area. Bass are a popular game fish in the area supporting fishing tournaments.

Channel & White Catfish (Ictalurus punctatus & Ameiurus catus): Channel and white catfish are omnivorous fish found in freshwater rivers, streams, ponds and lakes. During their lifetime, they may feed on insects, crustaceans (including crayfish), mollusks and fish (DeMort 1990). Male will build and guard the nest and fry. Both catfish species are important in benthic food webs that occur in the freshwater sections of the LSJR. Catfish are commercially and recreationally important in SJR.

Striped Mullet (Mugil cephalus): Striped mullet are detritivores that can live in a wide salinity range. They are abundant in most of the SJR, closely associated with bottom mud and feeding on algae, and decaying plant material. Mullet spawn offshore and their larvae drift back into the SJR estuary. They help to transfer energy from detrital matter that they feed on to their predators – 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 have significant recreational value as food and bait.

Southern Flounder (Paralichthys lethostigma): These are another common fish in the SJR estuary that are bottom-dwelling predators that eat shrimp, crabs, snails, bivalves and small fish. After spawning offshore in fall and winter, the larvae drift as part of the plankton eventually being transported back to the estuary to settle and grow. They are important in maintaining ecological balance in their roles as both predator and prey. They are food for sharks, marine mammals and birds. Flounders are important both commercially and recreationally in SJR.

Sheepshead (Archosargus probatocephalus): These fish are common to the SJR estuary and coastal waters. They prey on bivalves, crabs and barnacles. The fish spawn off shore in spring and the developing larvae are carried back to the coast by currents. The larvae enter the inlets and settle in shallow grassy areas. These fish are important in maintaining the estuarine and coastal food web as both a predator and prey. Sheepshead are prey for sharks and marine mammals. They are ecologically, recreationally and commercially important.

Atlantic Croaker (Micropogonias undulatus): These are bottom-dwelling predators common around rocks and pilings in the estuary. Spawning takes place in winter and spring in offshore waters, and planktonic offspring are transported back inshore to settle in vegetated shallow marsh areas. Croakers are important in the food web as both predator and particularly as prey. They feed on small invertebrates, and are fed on by fish, such as red drum, seatrout, and sharks. These fish support significant commercial and recreational fisheries in LSJR.

Baitfish (multiple species): There are more than two-dozen small schooling species like anchovies, menhaden, herring, killifish, sheepshead minnows, and sardines. Many baitfish species play a vital role in the ecosystem as planktivores. Others eat small crabs, worms, shrimp and fish. Most spawning occurs at inlets or offshore. Most migrate along or away from the shore. When the larvae hatch they are transported back to the estuary where they grow. Baitfish are important as prey for many larger fish species. They are also important as omnivores that recycle plant and/or animal material making that energy available to higher trophic levels. Commercial uses include bait fish, such as anchovy, menhaden, sardines, and herring which are converted into fertilizers, fishmeal, oil, and pet food (FWC 2000). Smaller fisheries catch killifish, sheepshead minnows, and sardines. For more information see Section 3 Fisheries and Appendix 3. Submerged Aquatic Vegetation (SAV)

Submerged aquatic vegetation provides nursery habitat for a variety of aquatic life, helps to reduce erosion, and limits turbidity by trapping sediment. Sunlight is vital for good growth of submerged grasses. Sunlight penetration may be reduced because of increased turbidity, pollution from upland development and/or disturbance of soils. Deteriorating water quality, which may include unusual increases in salinity has been shown to cause a reduction in the amount of viable SAV in an area. This leads to erosion and further deterioration of water quality.

Historical accounts indicate that SAV beds existed in the river since 1773 (Bartram 1928– in 1955 Edition). These SAV beds have shown a gradual decline likely due to a number of cumulative impacts including routine dredging, harbor deepening, filling of wetlands, bulk heading and construction of seawalls, water withdrawals, pumping from wells, along with the contributions from chemical contamination, and sediment and nutrient loading that comes from upland development (DeMort 1990; Dobberfuhl 2007).

Commonly found SAV species within the salinity transition zone in LSJR include: tape grass (Vallisneria americana), wigeon grass (Ruppia maritime), and southern naiad (Najas guadalupensis). The greatest distribution of SAVs in Duval County is in waters south of the Fuller Warren Bridge (Kinnaird 1983a). There are about eight other freshwater species in LSJR (IFAS 2007; Sagan 2007; USDA 2013). These species are all likely to be adversely impacted by increases in salinity.

Under controlled laboratory conditions, tape grass has been shown to grow in 0 to 12 parts per thousand (ppt) of salinity and survive for short periods of time in waters with salinities up to 15‐20 ppt (Twilley and Barko 1990; Boustany et al. 2003). However, SAV requires more light in a higher salinity environment due to increased metabolic demands (Dobberfuhl 2007). Evidence suggests that greater light availability can lessen the impact of high salinity on SAV (Kraemer et al. 1999; French and Moore 2003). What is not clearly understood is the ability of SAV to survive higher salinities when combined with environmental variables like temperature, turbidity, and excessive nutrients.

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 species, including the endangered Florida manatee (Trichechus manatus latirostris) (White et al. 2002). Manatees consume from four to 11% of their body weight in SAV daily (Lomolino 1977; Bengtson 1981; Best 1981; Burns Jr et al. 1997).

Commercial and recreational fisheries, including largemouth bass, catfish, blue crabs, and shrimp, are sustained by healthy SAV habitat (Watkins 1992). Fish and insects forage and avoid predation within the cover of the grass beds (Batzer and Wissinger 1996; Jordan et al. 1996). For example, Jordan 2000 mentioned that SAV beds in the Lower Basin have three times greater fish abundance and 15 times greater invertebrate abundance than do adjacent sand flats.

The section of the St. Johns River north of Palatka had relatively stable trends with normal seasonal fluctuations. The availability of tape grass decreased significantly in the LSJRB during 2000‐2001, because the drought caused higher than usual salinity values. In 2003, environmental conditions returned to a more normal rainfall pattern. As a result, lower salinity values favored tape grass growth again. 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). Sagan 2007 notes that at one of her monitoring sites, Sadler Point (the most seaward of all of her monitoring sites), SAV was present in 1998, but after a decline due to drought did not recover as did other SAV beds in the river. She cautions that long-term changes in salinity may be stressing SAV in the estuarine portions of the river. Declining SAV in the river south of Palatka and Crescent Lake is highly influenced by runoff and consequent increases in color of the water.

SAV response to drought and/or periods of reduced flow can provide crucial understanding as to how water withdrawals, harbor deepening and/or the issue of future sea level rise will likely affect the health of the ecosystem by adversely altering salinity profiles. For more information see Section 4.1 SAV and Appendix Florida Manatee

The Florida manatee (Trichechus manatus latirostris) inhabits the waters of the St. Johns River year-round. Manatees are generally most abundant in the LSJR from late April through August, with few manatees observed during the winter months (December-February). Manatees are protected under State and Federal Laws:  In 1967, under a law that preceded the Endangered Species Act of 1973 the manatee was listed as an endangered species. Manatees are also protected at the Federal level under the Marine Mammal Protection Act of 1972 (Congress 1972b) and at the State level under the Florida Manatee Sanctuary Act of 1978 (FWC 1978). The current federal status of the manatee is “Threatened” (March 30, 2016) having just been down listed by USFWS from “Endangered.”

Jacksonville University has conducted aerial surveys of manatees from 1994 to 2016. Within the SJR manatees were found in greater numbers south of the Fuller Warren Bridge where their food supply is greatest relative to other areas in Duval County. The SJR provides habitat for the manatee along with supporting tremendous recreational and industrial vessel usage. Watercraft deaths of manatees continue to be the most significant threat to survival. Boat traffic in the river is diverse and includes port facilities for large industrial and commercial shippers, commercial fishing, sport fishing and recreational activity. Also, in order to accommodate larger cargo ships more dredging by the port is expected in the future (Appendix Salinity). Dredging and/or deepening the channel can also affect the salinity conditions in the estuary by causing the salt water wedge to move further upstream (Sucsy 2008), negatively impacting biological communities like the tape grass beds on which manatees rely for food (Twilley and Barko 1990).

The average numbers of manatees observed on aerial surveys in the salinity transition zone area of the SJR decreased during periods of drought (1994-2000 and 2006-2009) and then increased again after the droughts (2000-2005 and 2009-2012) (Section 4.4). The reason for this was that during droughts elevated salinity leads to demise in the grasses that manatees feed on. As a result, manatees leave the study area in search for food. Freshwater withdrawals, in addition to harbor deepening, will alter salinity regimes in the LSJRB; however, it is not known yet by how much. 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. Data Sources & Limitations

Various sources of data were identified from DEP’s STORET database, SJRWMD, USGS and COJ. Monthly data obtained from The City of Jacksonville’s Environmental Quality Division “River Run” sampling program was used to determine salinity changes from 1991 to 2018. Other data sources identified include the City’s Station List (122 sites) data from 1995-2009; Tributaries (105 sites) data from 1995-2010; The River Run (10 sites) in the mainstem of SJR from 1980s to 2018; The Timucuan Run (12 Sites) in the Nassau and Ft. George area sampled every other month dating back to 1997; and the recently established Basin Management Action Plan (BMAP) Tributaries sites updated in October 2010. The latter consists of 10 Tributaries (with 2-3 sites each) for a total of 30 sites beginning in 2010.

In addition, there is Water Body ID (WBID) trend data available for Jacksonville from 1994-2018. Older data includes chlorides levels collected at Main Street Bridge from 1954 to 1965 as part of the city’s pollution sampling program around the time of the Buckman sewage plant coming on line (Hendrickson 2014).

Data obtained from The City of Jacksonville’s Environmental Quality Division “River Run” sampling program was used to determine salinity changes from 1991-2018. Data is collected about twice a month at the surface (0.5 m), middle (3-5 m), and bottom (5-10 m) in the water column. However, in recent years the sampling frequency has been significantly curtailed due to budget cuts. Four sites were chosen from the regular ten sampling stations.

      1. West bank of SJR 1000 m south of Doctors Lake;
      2. East bank of SJR 200 m north of a large apartment complex near Jacksonville University;
      3. South bank of SJR just west of Dames Point Bridge, near the western most range marker;
      4. Mainstem of SJR Mid channel N. of Piney Pt. 100 m west of green marker 5.

Kendall’s Tau correlation analysis revealed that salinity over time had significantly increased at the bottom, middle and surface at SJR near Doctors Lake, Piney Point mid-river, near Jacksonville University and Dames Point Bridge. For a map of the sample sites, analysis results, and graphs showing these trends, see Figures 8-20 in Appendix Salinity.

Monthly data are limited in that the sampling frequency is relatively low, and short-term events in weather may not be well represented. Continuous water quality data are available on the web through the USGS (USGS 2019). Currently active stations include the Dames Point Bridge, Buckman Bridge (Figure 2.62), Durbin Creek, Cedar River, Downtown Jacksonville, Pottsburg Creek, Broward River, Dunn Creek, Julington Creek, Ortega River, Christopher Creek, Marco Landing, Trout River, Clapboard Creek (Duval Co.), Shands Bridge (Clay Co.), Buffalo Bluff and Dancy Point (Putnam Co.), and Racy Point (St. Johns Co.) Other non-active stations for which data is available include Main Street Bridge and Shands Bridge. Yet, another new source for continuous data in LSJR includes NOAA’s PORTS program (NOAA 2019b). This data has some gap years due to budget cuts preventing collection, and some sites have been discontinued but salinity data is available for Mayport and Racy Point. Data at the Buckman Bridge show an increasing salinity trend in surface waters from 1995-2002 (represents a period of drought), then no data was available from 2004-2007, followed by another increasing trend from October 2008 – May 2013 (represents a period of drought). Then this was followed by an increasing trend in salinity from June 2013 to March 2018, in spite of another data gap from April to September 2015 (representing increased rainfall initially, and then the onset of drought conditions). In 2017, there was a severe drought early in the year, followed by strong storm and precipitation activity in late 2017. The region experienced above average rainfall in 2018, and this significantly reduced the salinity in the river for several months. These data indicate that large salinity fluctuations occurred and persisted for some time.

Figure 2.62 Surface salinity for June 1995- November 2002; October 2008-May 2013; June 2013-March 2018; and January 2017- January 2019 from USGS continuous data recording station at the Buckman Bridge.
Figure 2.62 Surface salinity for June 1995- November 2002; October 2008-May 2013; June 2013-March 2018; and January 2017- January 2019 from USGS continuous data recording station at the Buckman Bridge.

2.8.3. Overall Assessment (Ratings of Status and Trend)

The salinity regime in the LSJRB has changed over the years due to various human activities and natural phenomena, including rising sea level. The river’s ecology has been changed as a result of long-term rising salinity. In addition, there is no regulatory target for salinity in various sections of the river. However, this does not mean that we are not responsible for considering the environmental impacts of activities like surface water withdrawals and dredging, or future changes in rainfall and the amount and quality of surface water runoff given increases in population. The recent storms over the past two years are a temporary anomaly that contributed much freshwater to the system. This caused a decrease in salinity for some considerable time. All considered, including the historical and present values and trends in salinity, the current STATUS of salinity is rated as Unsatisfactory because of its impacts, and the TREND of salinity is rated as Worsening because it is increasing.

Water Quality, Fisheries, Aquatic Life, & Contaminants