Long before the arrival of European colonists, Indigenous people settled along the St. Johns River, using the waterway for transportation and commerce, harvesting resources for food and raw materials.  In the last five hundred years, European colonizers and American settlers have also used this important waterway as a fishery, means for travel and commerce, tourist destination, and source of recreation (Miller 1998; Belleville 2020; Crooks 2004; UNF 2019). More recently, however, scientists, politicians, and other stakeholders have increasingly recognized that the LSJRB is an ecologically vulnerable watershed, threatened by rising salinity, dredging activities that deepen the channel to attract larger cargo ships, numerous sources of pollution, and other environmental hazards (Crooks 2004; State of the River Report Sections 2, 4, and 5).

The St. Johns River flows north, from its headwaters in the marshes of Indian River County, to the Atlantic Ocean near Jacksonville (SJRWMD 2020c) (Figure 1.2). For management purposes, the entire St. Johns River watershed is commonly divided into five basins: the Upper Basin (southern, marshy headwaters in east central Florida); the Middle Basin (the area in central Florida where the river widens, forming Lakes Harney, Jesup, and Monroe); the Lake George Basin (the area between the confluence of the Wekiva River and St. Johns River, and that of the Ocklawaha River and the St. Johns River); the Lower Basin (the area in northeast Florida); and the Ocklawaha River Basin (the primary tributary for the St. Johns River).
The State of the River Report focuses on the Lower Basin (SJRWMD 2020e), which for management purposes is subdivided into 11 planning districts (see Figure 1.3).

This report defines the LSJRB in accordance with the SJRWMD definition: “that portion of the St. Johns River that extends from the confluence of the St. Johns and Ocklawaha rivers near Welaka north to the mouth of the St. Johns River at Mayport in Jacksonville” (SJRWMD 2008; Figure 1.1).

The LSJRB includes portions of six counties: Clay, Duval, Flagler, Putnam, St. Johns, and Volusia (Brody 1994; Figure 1.4). Notable municipalities within the Lower Basin include Jacksonville, Orange Park, Middleburg, Green Cove Springs, and Palatka.

The LSJRB covers a 1.8 million-acre drainage area, extends 101 miles in length, and has a surface area of water approximately equal to 115 square miles (Adamus et al. 1997; Magley and Joyner 2008).

1.2.1. Land Use and Land Cover

Based on the latest available land-use land-cover data for LSJRB (USDA 2022), wetlands and deep-water habitats made up 1/3 (32%) of the basin, forested areas another 1/3 (34%), urban areas 21%, agricultural land 8%, and the remaining 5% was classified as rangeland and barren land. See Figure 1.5 and Appendix 1.2.2 for detailed land use, land cover data since the 1970s.

The urban, built-up percentage of the region will likely increase in future years as North Florida continues to grow (SJRWMD 2008; NRC 2010).

1.2.2. Ecological Zones

The LSJRB is commonly divided into three ecological zones based on expected salinity differences (Hendrickson and Konwinski 1998; Malecki et al. 2004), see Figure 1.6. The mesohaline riverine zone is the most northern ecological zone in the LSJRB, stretching generally from the Atlantic Ocean to the Fuller Warren Bridge. This section of the river is narrower, deeper and well-mixed with an average salinity of 14.5 parts per thousand (ppt).  Current trends show decreasing salinity in the bottom part of the river at the Dames Point Bridge location. Increased precipitation and freshwater inflows possibly explain this (State of the River Report Section 2.8; Appendix 4.1.7.1.F. Salinity).

South of the Fuller Warren Bridge, the St. Johns River widens into a broad, shallow, slow-moving, tidal area called the oligohaline lacustrine zone. This section extends generally from the Fuller Warren Bridge to south of Doctors Lake and has an average salinity of 2.9 ppt. Recent findings confirm that salinity has significantly increased over time at the bottom, middle and surface of the mid-river section (State of the River Report Section 2.8; Appendix 4.1.7.1.F Salinity).

South of Doctors Lake to the confluence of the St. Johns and Ocklawaha rivers near Welaka, the LSJRB transitions into the freshwater lacustrine zone. This zone stretches through the Middle and Upper Basins of the St. Johns River as well (State of the River Report Sections 2.8 and 4.1). The zone where saline river water begins to mix with freshwater has moved south into here in the last few decades, likely the result of anthropogenic changes to the river (Monroe and Hong 2018; Rivers 2022). The freshwater lacustrine zone is lake-like, has an average salinity of 0.5 ppt, and experiences tidal fluctuations that are lower than those observed in the other ecological zones (State of the River Report Section 2.8). According to the data from 10 monitoring stations, the overall trend shows long-term increased salinity (Appendix 4.1.7.1.F Salinity).

1.2.3. Unique Physical Features

The St. Johns River possesses distinct exceptional physical features.

The St. Johns River is the longest river in Florida. Stretching 310 miles and draining approximately 9,430 square miles, this extensive river basin drains about 16% of the total surface area of Florida (DeMort 1990; Morris IV 1995).

The St. Johns River flows northward. The St. Johns River flows slowly northward because its headwaters to the south lie at a slightly higher elevation than the mouth at Mayport, where the river enters the Atlantic Ocean (SJRWMD 2020c). Therefore, the Upper St. Johns lies south of the Lower St. Johns (DeMort 1990).

The St. Johns River is one of the flattest major rivers in North America. The headwaters of the St. Johns River are less than 30 feet above sea level. The river flows downward on a slope ranging from as low as 0.002% (Benke and Cushing 2005) to about 1% (DeMort 1990) see Figure 1.7. This extremely low gradient contributes to a typically slow flow of the St. Johns River. This holds back drainage, slows flushing of pollutants, and intensifies flooding and pooling of water along the river, creating numerous lakes and extensive wetlands throughout the drainage basin (Durako et al. 1988). Low lying areas of northeast Florida are especially vulnerable to flooding during the June through November rainy season, during “king tides,” and during storms (COJ 2020b; SJRWMD 2020b; NWS 2021). Massive flooding occurred in the fall of 2017, when the storm surge from Hurricane Irma flooded wide areas of the LSJRB for weeks (NOAA 2018). The retention time of the water, and of dissolved and suspended components in the river last three to four months (Benke and Cushing 2005). In addition, estuarine systems like the St. Johns River tend to concentrate certain pollutants due to high retention times of water (Durako et al. 1988). For a discussion of measures to mitigate flooding, see 1.5.4 of this chapter, under “Other Issues.”

The Lower St. Johns River is a broad, shallow system. The average width of the St. Johns River from Lake George to Mayport is one mile, although the floodplain reaches a maximum width of ten miles (Miller 1998). The variability in width can result in different water flow patterns and conditions on opposing banks of the river (Welsh 2008).  Through the year 2000, the average depth of the river was about 11 feet (Dame et al. 2000), though today the figure has increased due to the deepening of the shipping channel.  Jaxport is the state’s largest container port, and through the harbor deepening project that began in 2018 and concluded in May 2022, the shipping channel was deepened from 40 feet (12.2 meters) to 47 feet (14.3 meters) to accommodate post-Panamax vessels (Rivers 2022; JAXPORT 2022b).

The St. Johns River drains into the Atlantic Ocean. The average discharge of water at the mouth of the St. Johns River is 8,300 cubic feet per second (235 cubic meters/second) (Miller 1998) or 5.4 billion gallons per day (Steinbrecher 2008). By contrast, the Mississippi River’s discharge is about 593,000 cubic feet per second (16,792 cubic meters/second) (USCB 2011).

The tidal flow at the mouth of the St. Johns River is much higher, about seven times greater, than the freshwater discharge (Anderson and Goolsby 1973). This difference often causes “reverse flow,” or a southward flow, up the river. Reverse flow has been detected as far south as Lake Monroe, 160 miles upstream, and is also influenced by weather conditions such as drought and by ocean tides (Durako et al. 1988). Natural water sources for the St. Johns River are direct rainfall, run-off from rainfall, underground aquifers, and springs. Continual input from springs and aquifers supplies the river with water that discharges into the Atlantic Ocean, despite drought periods or seasonal declines in rainfall (Benke and Cushing 2005). Water quality depends on a variety of factors, including land use along the St. Johns River, infrastructure maintenance, weather patterns, and various other factors (State of the River Report Section 2).

The Lower St. Johns River is a tidal system with an extended estuary. The tidal range at the mouth of the river at Mayport, Florida is about six feet (McCully 2006). The Atlantic Ocean’s tide heights are large compared to the slope of the St. Johns River, and at times can produce strong tidal currents and mixing in the northernmost portion of the river. The St. Johns River is typically influenced by tides as far south as Lake George, 106 miles upstream (Durako et al. 1988). Tidal reverse flows occur daily in the Lower St. Johns River, and net reverse flows, as much influenced by winds as by tides, can occur for weeks at a time (Morris IV 1995).

The St. Johns River receives saltwater from springs. Several naturally salty springs flow into this watershed. The most significant inputs of salty spring water originate from Blue Springs, Salt Springs, Silver Glen Springs, and Croaker Hole Spring (Campbell 2009). Inputs from these salty springs cause localized areas of elevated salinity (>5 ppt) in otherwise freshwater sections of the river (Benke and Cushing 2005). The amount of flow from springs is highly variable and dramatically affected by droughts (Campbell 2009).

The salinity of the St. Johns River is also affected by seasonal rainfall patterns and episodic storm and drought events. In general, there is a predictable seasonal pattern of freshwater input from rainfall into the Lower St. Johns River, with the majority of rain falling during the wet season from June to October (Rao et al. 1989, see Figure 1.8). However, this seasonal pattern of rainfall can be overridden by less predictable, episodic storm events, i.e., tropical storms, nor’easters, hurricanes (such as Matthew in 2016 and Irma in 2017), and droughts (such as those of the early 1970s, early 1980s, 1989-1990, and 1999-2001) (DEP 2010e; SJRWMD 2016a; SJRWMD 2017b). Surges of freshwater from heavy rainfall tend to reduce salinity levels in the river and introduce pollutants from impaired creeks. Hurricane Irma, which dumped 2.2 trillion gallons of water on northeast Florida in September 2017, lowered the salinity of the St. Johns River for weeks afterward. Likewise, periods of drought can raise the salinity of the river as highly saline water replaces freshwater normally provided by rainfall and other sources (State of the River Report Section 2.8; White 2017; SJRWMD 2017c). Thus, rainfall patterns can prompt a chain of events in the river, leading to impacts on aquatic plants and animals. Simplified examples of several sequenced events are illustrated in Figure 1.9.

 

The St. Johns River can be influenced by local wind direction. While ocean winds affect the river’s flow, local winds create surface stress upon the river, which can enhance the flow. South winds blowing to the north accelerate the flow of water toward the ocean if the flow is not opposed by a strong tidal current. Such strong southerly winds occurred during Hurricane Irma in 2017, resulting in major flooding in the LSJRB (NOAA 2018). Similarly, north winds can push river water back upstream (Welsh 2008). Strong sustained north winds from fall nor’easters or summer hurricanes can push saltwater up the river into areas that are usually fresh. Although considered a natural occurrence, reverse flow of the river can affect flora and fauna with low salinity tolerances and cause inland areas to flood (State of the River Report Sections 2.8 and 4.1).

The St. Johns River is a dark, black water river. Southern black water rivers are naturally colored by dissolved organic matter derived from their connections to swamps, where plant materials slowly decay and release these materials into the water (State of the River Report Section 4.1.1; Brody 1994). The Dissolved Organic Matter (DOM) limits light penetration, and therefore photosynthesis, to a very shallow layer near the surface of the river.

The St. Johns River is affected by anthropogenic changes and climate change. Several anthropogenic factors—including sea level rise and dredging—have increased salinity in the LSJR and moved the location, where saltwater and freshwater mix to the south. As noted in Section 2.8, factors like “reduced freshwater inflows to the river caused by dams, surface water withdrawals, or significant pumping of ground water” can also increase salinity in the long run (State of the River Report Section 2.8, especially 2.8.2, and 4.1).  The Army Corps of Engineers (ACOE) acknowledge that its project to deepen the St. Johns River to 47 feet near Jacksonville could increase water levels in a 100-year storm surge by 3 to 6 inches, and up to 8 inches in isolated locations (USACE 2018). A recent study also suggests that dredging activities since the 1890s likely increased the storm surge associated with Hurricane Irma in 2017 (Talke et al. 2021a).