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Water bodies, watersheds and storm water

Lower St. Johns River Basin

In the lower basin of the St. Johns River (that portion of the watershed from Lake George to the river’s mouth at Mayport), a wide variety of everyday activities inadvertently add nitrogen and phosphorus, essential plant nutrients, to surface waters. In fact, in an average year, approximately 15 million pounds of nitrogen pollution and 1.8 million pounds of phosphorus pollution (or 1,680 dump trucks carrying 10,000 pounds each) enter the river between Palatka and the river’s mouth.

Location of Lower St. Johns River Basin

Treated wastewater is the largest contributor of nutrient pollution in the lower St. Johns River. This partially treated sewage is treated and disinfected in wastewater utilities, then, often times, is pumped to the St. Johns River for disposal. Other significant nutrient pollution sources include farms in the agricultural areas of Flagler, Putnam and St. Johns counties, carrying animal wastes, fertilizers and pesticides into the waterway through canals, ditches and streams that lead to the river.

Storm water from urban and suburban areas sends lawn fertilizers, sediments, pesticides, roadway grease and trash into the river and its tributaries. Storm water contributes the majority of the toxic trace metals — such as copper, lead and cadmium — that enter Florida waters and the lower St. Johns River. The upstream watersheds of the river (the upper and middle St. Johns River basins) also contribute significant amounts of nitrogen and phosphorus to Lake George and the lower St. Johns River. The nutrient-rich discharges into the river have fed harmful algal blooms, which can concentrate with wind and tide to create aesthetically unappealing and occasionally foul-smelling shoreline mats. Such blooms can also harm the environment by blocking sunlight to submerged aquatic plants, deplete dissolved oxygen, and impact fish and other wildlife by reducing the quality of the aquatic food chain, and on occasion, producing algal toxins.

These pollutants currently exceed the amount that the lower St. Johns River can receive and still meet state and federal water quality standards.


From the air, the St. Johns River appears to snake among the trees along its shoreline.

From the air, the St. Johns River appears to snake among the trees along its shoreline.

From the air, the St. Johns River appears to snake among the trees along its shoreline.

From the air, the St. Johns River appears to snake among the trees along its shoreline.

Florida’s Surface Water Improvement and Manage­ment (SWIM) Act directed the St. Johns River Water Management District to conduct the necessary research to gain an under­standing of what is needed to restore and properly manage the river, and to develop a plan for that work.

The district has formed partnerships over the years with local governments, other agencies, stakeholder groups and the public to develop initiatives to restore the river, including the 1998–2003 River Agenda and the 2006 River Accord.

The investments by the district and its partners are the largest in the lower St. Johns River’s history and include a citywide no net-gain goal for septic tanks (Jacksonville/Duval County), a program to improve access to the river, an annual state of the river report and a research program to examine why the river’s tributaries are filling in with silt.

Examples of the many projects either completed or under way include:

  • The district’s rough fish harvest was designed and implemented to meet downstream nutrient load reductions and reduce the severity of algal blooms in the lower St. Johns River. Utilizing $1.7 million in legislative appropriations over the last two years, approximately 20,000 pounds of phosphorus and 53,000 pounds of nitrogen have been removed from Lake George in Volusia, Putnam and Marion counties. In 2014, the May to September harvest removed more than 11,000 pounds of phosphorus and 29,000 pounds of nitrogen. The 2015 harvest, conducted with legislative appropriations for St. Johns River restoration and protection, removed 9,000 pounds of phosphorus and 27,000 pounds of nitrogen. Removing gizzard shad from Lake George will help to meet the necessary downstream nutrient loading reduction essential to meeting state water quality standards and reduce the severity of algal blooms in the lower St. Johns River.
  • JEA’s $32 million worth of completed and ongoing projects upgrade existing reclaimed water plants, provide reclaimed water for irrigation at golf courses and office parks, and make improvements to infrastructure to accommodate expanded reuse. Nutrient pollution removed from the river: 556,000 pounds/year. Discharge eliminated: 21 million gallons per day (mgd).
  • Clay County Utility Authority (CCUA) launched operation of nine rapid infiltration basins at CCUA’s Mid-Clay Wastewater Treatment Facility in February 2016, improving river water quality and reducing demands on the aquifer system. The project effectively eliminates wastewater discharges to the St. Johns River. Project benefits will include storing reclaimed water during wet periods for use during the dry months and reducing nitrogen to the lower St. Johns River by more than 19,000 pounds per year. The new basins allow the Mid-Clay facility to handle more than 2 million gallons of reclaimed water a day. Reclaimed water is stored and treated in a series of nine infiltration cells, where it percolates into the surficial aquifer. The recaptured water is pumped to CCUA’s adjoining reclaimed water distribution system and used to augment the reclaimed water system. By redesigning the project in 2014 from an aboveground reservoir to the current footprint, CCUA saved taxpayers more than $1.6 million from the original cost estimate.
  • Naval Air Station Jacksonville (NAS-Jax) launched its reclaimed water facility in October 2015. This project has far-reaching benefits, removing all of the NAS-Jax treated wastewater from the St. Johns River and reusing that water at NAS-Jax. Specifically, it eliminates 315 million gallons a year of wastewater effluent discharges to the river and approximately 45,000 lbs/yr of total nitrogen. With this “zero discharge,” NAS-Jax will exceed its anticipated state requirements to reduce phosphorus entering waterways. The project also will reduce groundwater withdrawals from the Floridan aquifer by 48 million gallons a year. The district provided $1.8 million in funds toward this collaborative effort. In addition the U.S. Navy, the city of Jacksonville was a funding partner.
  • Palatka expanded reclaimed water to the city’s golf course, Ravine State Gardens and various recreational ball fields, ultimately removing all discharges from the river at a cost of $8.5 million. Completed in September 2012, the estimated total nitrogen reduction to the St. Johns River was 158,600 pounds per year and estimated total phosphorus reduction was 21,100 pounds per year.
The Jacksonville skyline along the St. Johns River.

The Jacksonville skyline along the St. Johns River.

The district is also engaged with the Florida Department of Agriculture and Consumer Services, Florida Depart­ment of Environmental Protection, Natural Resources Conservation Service, University of Florida’s Institute of Food and Agricultural Sciences and the Northeast Florida Growers Association in the Tri-County Agricultural Area (TCAA) Water Management Partnership. Partnership objectives are to contribute to the improved health of the lower St. Johns River through on-farm and regional water management projects and practices that reduce the movement of nutrients to the river, improve water conservation, and result in more efficient farm management while maintaining the long-term viability of agriculture in the TCAA.


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St. Johns River Water Management District
4049 Reid Street, Palatka, FL 32177
(800) 725-5922