Jacksonville, Florida, is the largest city by land area in the contiguous United States — 875 square miles of sprawling development across Duval County. That sprawl, combined with a massive military presence and unique hydrogeology, creates a water quality picture that’s distinctly Jacksonville.
JEA (formerly Jacksonville Electric Authority) provides water to approximately 500,000 connections in the Jacksonville area. Unlike most major Florida cities that have consolidated onto centralized treatment systems, Jacksonville still has a significant number of areas served by private wells and septic systems — a legacy of the city-county consolidation in 1968 that merged urban Jacksonville with sprawling rural Duval County.
JEA draws entirely from the Floridan Aquifer, operating over 130 water supply wells across the system. This is groundwater — not surface water — which has different quality characteristics and vulnerability profiles than surface water systems.
PFAS: Multiple Military Sources
Jacksonville’s PFAS contamination is among the most significant in Florida, driven by multiple military installations:
NAS Jacksonville — One of the Navy’s largest air stations, located on the west bank of the St. Johns River in urban Jacksonville. Decades of AFFF use for aviation firefighting have contaminated groundwater beneath and around the base. The contamination plume extends into surrounding neighborhoods, and PFAS has been detected in private wells near the installation.
Naval Station Mayport — Located at the mouth of the St. Johns River, Mayport is a major fleet concentration area with documented AFFF use and PFAS contamination.
Cecil Commerce Center (former NAS Cecil Field) — Closed in 1999, this former naval air station on Jacksonville’s westside has extensive PFAS contamination from historical AFFF use. The base is now being redeveloped as a commerce center, but the groundwater contamination remains.
Camp Blanding Joint Training Center — Located about 35 miles southwest of Jacksonville in Clay County, this National Guard facility has PFAS contamination affecting nearby communities.
The cumulative effect: PFAS is present in groundwater across multiple areas of Jacksonville and surrounding counties. For JEA’s well-based supply system, this is particularly concerning because groundwater is the direct source — there’s no surface water treatment step that might dilute or partially remove PFAS.
JEA has been testing under UCMR 5 and monitoring wells near known contamination sources. Some wells have been taken offline, and the utility is evaluating treatment options to meet EPA’s 2024 MCLs.
The Floridan Aquifer in Jacksonville
Jacksonville sits over the Floridan Aquifer — one of the most productive aquifer systems in the world. In northeast Florida, the aquifer provides abundant, relatively cool groundwater that requires less treatment than surface water.
Typical treatment for JEA’s well water includes aeration (to remove hydrogen sulfide — the “rotten egg” smell common in Florida groundwater), disinfection, and fluoridation. Some wells also require treatment for iron and hardness.
Aquifer vulnerabilities in the Jacksonville area:
- Saltwater intrusion — Jacksonville’s coastal location means the freshwater-saltwater interface is a constant concern. Over-pumping can pull saltwater into wells.
- Surficial contamination — In areas where the confining clay layer is thin or absent, surface pollutants can reach the Floridan relatively quickly.
- PFAS migration — PFAS compounds are highly mobile in groundwater and can travel long distances in the Floridan’s permeable limestone.
- Sinkholes — Northeast Florida’s karst geology means sinkholes can create direct conduits between the surface and the aquifer.
Septic Systems: Jacksonville’s Hidden Problem
Jacksonville has an estimated 80,000 to 100,000 septic systems — one of the highest concentrations of any major American city. Many of these systems are in areas with:
- High water tables
- Sandy, permeable soils that provide minimal filtration
- Proximity to waterways and the aquifer recharge zone
Failing and aging septic systems contribute nitrogen, phosphorus, bacteria, and pharmaceuticals to both surface water and groundwater. The connection is documented: neighborhoods with high septic density show elevated nutrient levels in nearby waterways and, in some cases, in shallow groundwater.
Jacksonville’s septic-to-sewer conversion program has been expanding centralized sewer service to replace septic systems, but the scale of the problem — 80,000+ systems — and the cost of connection (often $10,000-$20,000+ per property) mean progress is measured in decades.
The St. Johns River
The St. Johns River — one of the few major US rivers that flows north — runs through the heart of Jacksonville. While JEA doesn’t use the St. Johns as a drinking water source, the river’s water quality is closely connected to the city’s environmental health:
- CSO and SSO events discharge untreated or partially treated sewage into the river
- Stormwater runoff from Jacksonville’s vast impervious surfaces carries pollutants into the St. Johns
- Algal blooms in the river are fueled by nutrient loading from development, agriculture, and septic systems
- Fish consumption advisories have been issued for certain species in the St. Johns due to mercury and other contaminants
What Jacksonville Residents Should Know
- Know your water source. If you’re on JEA, you’re on treated Floridan Aquifer groundwater. If you’re on a private well, you’re drawing from the same aquifer — but without JEA’s treatment and monitoring.
- Private well owners — TEST YOUR WATER. This is critical in Jacksonville given the military PFAS sources, septic system density, and aquifer vulnerability. Test for PFAS, bacteria, nitrates, and arsenic at minimum. If you’re near NAS Jacksonville, Mayport, or Cecil Field, PFAS testing is especially important.
- If you’re on septic — maintain your system. Regular pumping, avoiding flushing non-degradable items, and monitoring your drain field all reduce your impact on groundwater.
- Consider filtration. A reverse osmosis system removes PFAS, hardness, and most other contaminants of concern. For the “rotten egg” smell common in Florida well water, aeration or oxidation systems are effective.
- Read JEA’s water quality report for testing results specific to your service area.
Related Reading
- Tampa Water: Desalination and PFAS — Florida’s Gulf Coast faces parallel PFAS challenges.
- Miami Water: Biscayne Aquifer and Saltwater Intrusion — South Florida’s unique water vulnerability.
- Camp Lejeune Water Contamination — Military base contamination cases share common PFAS pathways.
- Virginia Beach Water: PFAS and Military Contamination — Another military community fighting PFAS contamination.
- Sarasota Water Quality and Wastewater Issues — Florida’s water infrastructure challenges from coast to coast.
The Bottom Line
Jacksonville’s water quality is shaped by three overlapping factors: extensive military PFAS contamination, a groundwater-dependent supply system that’s directly exposed to aquifer contamination, and a massive septic system legacy that degrades both surface water and groundwater.
The city is making progress on septic-to-sewer conversion and PFAS monitoring, but the scale of these challenges — 80,000+ septic systems, multiple military contamination plumes, and a sprawling city with 130+ supply wells — means solutions will take decades and billions of dollars.
If you’re concerned about your water quality, a certified water treatment professional can test your water and recommend the right treatment system for your home.