Jacksonville Water Quality: River, Creeks, Beaches and Tap Water

Jacksonville water is tested by four bodies: the city Environmental Quality Division for the St. Johns River and its creeks, the Florida Department of Health in Duval County for the beaches, and JEA for tap water, with FDEP reporting on the tributaries.

The split follows the water. The Jacksonville Environmental Quality Division runs the River Run program, a monthly sampling event at 10 stations in the mainstem of the St. Johns River, and a separate Tributary Program on the creeks (City of Jacksonville River Run). The FDEP Northeast District partners with the Duval County Health Department and the City of Jacksonville to produce quarterly water quality reports on the tributaries of the St. Johns River in Duval County (Duval Tributary Watch). Under that arrangement the health department permits septic tanks and issues health advisories, while the city monitors the water.

Last verified: October 15, 2026, on the City of Jacksonville, FDEP, Florida Department of Health and JEA websites.

Fecal coliform in the main stem of the St. Johns at Jacksonville is usually well below the State Water Quality Standard, FDEP says, but harmful algal blooms regularly occur in the lower river (FDEP; UNF State of the River guide).

Bacteria pollution was first documented in the St. Johns River in the 1950s. Eliminating direct sewage discharges and hundreds of small, inefficient sewage package plants dramatically lowered bacteria in the main stem, yet many sources remain because of the river's character and the density of Jacksonville's population (FDEP).

The public guide to the State of the River Report states that harmful algal blooms regularly occur in the LSJRB, made worse by excess nutrients, mainly nitrogen and phosphorus from commercial and residential fertilizing, and that salinity is rising significantly in some locations, possibly causing a loss of submerged aquatic vegetation (UNF State of the River guide). The report is written by researchers from Jacksonville University, the University of North Florida, Florida Southern College and Penn State Berks.

The River Run stations measure dissolved oxygen, pH, temperature, salinity and specific conductance in the field, and nutrients, chlorides, turbidity, suspended solids, color, biochemical oxygen demand, fecal coliform and, less often, certain metals in the lab, with data meant to help set Total Maximum Daily Loads for the Lower St. Johns in Duval County (City of Jacksonville).

FDEP says bacteria levels in many Duval County tributaries remain high, has identified tributaries impaired by fecal coliform, and reports on creek groups from the Ortega and Cedar rivers to the Trout River (Duval Tributary Watch).

The FDEP tributary reports group the Jacksonville creeks into areas: Ortega and Cedar River, Broward River and Dunn Creek, Julington and Durbin Creeks, rural tributaries, Pablo Creek with Greenfield and Mt. Pleasant Creeks, Mill Cove and Arlington, the Downtown Area Tributaries, the Southside and the Trout River (Duval Tributary Watch). As federal law requires, DEP has identified tributaries impaired by fecal coliform; Total Maximum Daily Loads are the water quality targets, based on state standards for specific pollutants. FDEP lists the bacteria sources as bypassed and failing septic tanks, stormwater runoff, sanitary sewer overflows, leaking sewer pipes, failing package wastewater treatment plants, livestock, pets and wild animals.

The city notes that pollution impacts in the tributaries can be pronounced because they have less dilution potential than larger water bodies, and the two key measurements at the roughly 100 Jacksonville tributary sites are dissolved oxygen and fecal coliform bacteria (City Tributary Program). Questions about health risk in a particular creek go to the Duval County Health Department, which FDEP names as the agency for that question.

Yes: the Florida Department of Health in Duval County samples ocean water biweekly from March through October along the shore from Jacksonville Beach north to Little Talbot Island (DOH-Duval).

The Duval samples are tested for bacteria and posted on the statewide Florida Department of Health beach water quality page; the county office takes questions at 904-253-1282 (Florida Department of Health in Duval County).

The state rates each result by enterococci per 100 milliliters of marine water: Good is 0 to 35, Moderate is 36 to 70, and Poor is 71 or greater (Florida Department of Health). An advisory is issued for a sampling site when an enterococci result exceeds 70 colony forming units per 100 milliliters of beach water sampled and a resample also exceeds that value. A practical point for a Jacksonville Beach or Atlantic Beach swim in November through February: the Duval program states its sampling season as March through October.

JEA tap water in Jacksonville comes from wells in the Floridan aquifer about 1,000 feet below land surface, and JEA's latest annual report covers testing from January 1 to December 31, 2025 (JEA 2025 Water Quality Report).

JEA pumps well water to treatment plants where an aerator removes the sulfur odor, then disinfects it with chlorine; two plants also use ozone. The JEA Major Grid supplies water to most of Duval County and the northwest part of St. Johns County, and JEA also lists the Mayport system and the Lofton Oaks, Ponte Vedra and Ponce de Leon grids (JEA).

FDEP source water assessments done in 2025 counted 173 potential contamination sources near Major Grid wells, at a low to moderate susceptibility level, and 2 near the Mayport system, at a low level. Jacksonville customers with questions about lead or who want water tested can call the JEA Water Quality line at 904-665-4521 or email [email protected] (JEA 2025 Water Quality Report).

Two Jacksonville river efforts are the JEA and city septic tank phase-out, approved by the City Council on August 23, 2016, and JEA's cuts in the nitrogen it discharges to the river under a state nutrient plan (JEA septic program).

The phase-out replaces septic systems with sewer service to keep nutrients out of the St. Johns River and other local waterways. Its first four areas are Biltmore C, Beverly Hills, Christobel and Riverview. Construction in Biltmore and Beverly Hills was completed in 2022 and 2024, respectively; a March 2026 update says Christobel construction has begun and Riverview passed its 70 percent participation requirement and is advancing into design (JEA). The same JEA page still says elsewhere that the Christobel project is expected to begin April 2026, a date it marks as highly subject to change, and that Riverview met the 70 percent requirement on November 10, 2025.

JEA reports that under the Basin Management Action Plan it was required to reduce its nitrogen discharge to the river from 1,450 tons per year in 1999 to 720 tons per year by the end of 2013, and it reports a reduction of over 60 percent from that high, well under the final limit (JEA St. Johns River page). Readers should note that the JEA page is dated: its newest figure is for 2014, and it gives that year's total as 77 tons in one place and 577 tons in another.

Two Jacksonville city pages also disagree on where the Ambient Water Quality Section sits: the Tributary Program page lists 214 N. Hogan Street, 5th floor, while the River Run page lists 407 North Laura St., Third Floor, both with (904) 255-7100 (City Tributary Program; River Run). Algal blooms are reported to FDEP at 855-305-3903 and chemical spills to the City of Jacksonville at 904-630-2489 (UNF guide).