Healthy Estuaries: A Look at Water Quality in the Pensacola Bay System

When I joined the Escambia County Extension office as the Sea Grant Agent in 2012, my advisory committee told me that water quality in the Pensacola Bay System was one of their largest concerns. When I asked what about the water concerned them the most, they responded with fish kills and health advisories. Since that time, I have tried to provide education to residents and businesses about the frequency of fish kills and health advisories, potential causes, and what they can do to reduce these. We began a program we called Bringing Back the Bayous having town-hall meetings with panels of experts to discuss these issues. I have since added a weekly report we call Sea Grant Notes that updates everyone on the current frequency of both.

Citizen scientists monitoring water quality on Bayou Texar.
Photo: Marine Science Academy Washington High School

Over the last nine years, fish kills have been very infrequent. Most reported by the Florida Fish and Wildlife (FWC) have been the result of discarded baitfish that washed ashore. That said, we continue to monitor nutrient levels every other month with our Lakewatch program. These six volunteers’ sample three stations in their assigned bodies of water – lower Perdido Bay, Big Lagoon, Bayou Grande, Bayou Chico, Bayou Texar, and Pensacola Bay.


The volunteers’ sample for total nitrogen, phosphorus, chlorophyll a, water clarity, and salinity. The connection between these nutrients and fish kills is eutrophication. Eutrophication is a process where excessive nutrients in the water produce algal blooms. The algae consume dissolved oxygen during the evening hours and, being short lived, cause large oxygen demand when bacteria decompose their cells from the natural die off. Low dissolved oxygen in the water can cause fish kills.


Though the Lakewatch Team is not monitoring dissolved oxygen, they are monitoring the nutrients and chlorophyll a (a proxy for algal abundance in the water column – an algal bloom). The levels of total nitrogen are high, particularly in Bayou Texar, but no large-scale fish kills have occurred in several years. There was a rather large kill in Bayou Chico in 2019, but it is important to remember that hypoxia (low levels of dissolved oxygen) can occur naturally and it was thought this kill was the result of extremely warm water during that summer. Warm water holds less dissolved oxygen.


The Marine Science Academy at Washington High School has been monitoring nutrients and dissolved oxygen within Bayou Texar for at least 10 years now. Their data can be accessed by visiting their website –

Links to most recent presentations


In terms of health advisories, these do still occur frequently. Many are connected with increase rainfall events producing increase health advisories. But not always. Between 2018 and 2020, the Florida Department of Health posted reports from 807 samples at 13 sites around the bay area. 189 (23%) had a POOR reading (indicating that the number of Enterococcus colonies exceeded the 71 colonies/100ml sample allowed). 137 of the 189 POOR readings (72%) scored POOR on a second sample and a health advisory was issued. This was 17% of the total samples collected between 2018 and 2020.


This seems to be a low number – 17% – but when you look at the sites where the POOR readings came from it show another part to this. Of the 13 sites monitored by FDOH, six (46%) had a poor reading – the other seven sites did not have a single poor reading in the last three years. Those six sites that did are not sampled at the same frequency. Bayou Texar and Sanders Beach are sampled weekly, year-round. However, Bayou’s Chico and Grande, and sites at Pensacola Beach and Perdido Key, are typically sampled once week from March through October. This is due to funding. They focus on beaches where people swim and during times when they swim. If you calculate the percent of health advisories / samples taken from these six sites you will see the bayous are a problem.


Percent of Samples Requiring a Health Advisory
Body of Water 2018 2019 2020
Bayou Texar 44% 32% 49%
Bayou Chico 60% 56% 60%
Bayou Grande 47% 28% 47%
Sanders Beach 11% 9% 11%
Park West Pensacola Beach 0% 4% 0%
Casino Beach Pensacola Beach 0% 4% 0%


2018 and 2020 saw higher than normal rainfall (normal average = 60” / year).

2019 saw lower than normal.

You will notice that the three bayous are around 30% or higher. And that both Bayou’s Texar and Grande fluctuated with the changing rainfall amounts. But Bayou Chico and Sanders Beach (at the mouth of Bayou Chico) did not. They remained relatively the same. This suggest that the advisories issued at the non-Chico sites are closer related to stormwater events and sanitary sewage overflows. The Chico site numbers suggest a steady source of release from locations yet to be determined. Bayou Chico is considered one of the FDEP’s BMAP sites (Basin Management Action Plan). These sites are deemed impaired at levels that action needs to be taken. Bayou Chico is a BMAP due to these bacteria levels. All agencies are trying to address these problems, but there are things residents and businesses can do as well.


  • Do not flush anything down the commode that is not sewage related – waste and toilet paper only. Many products advertised as “flushable” are flushable, but they are not biodegradable and thus cause clogs in the system. Which can lead to leaking septic systems and sanitary sewage overflows during heavy rains.
  • If you have a septic system, you need to be aware of flushing food and other items that can take a long time to break down. These can cause septic systems to leak as well.
  • Septic systems typically form “scum” on the surface (these are oils and grease), sludge on the bottom (these or solids that will decompose), and effluent water in between these two. The effluent typically leaves the tank and percolates into the drain field for further treatment. If the system is not inspected (and pumped) every 3-5 years, the “scum” and “sludge” can build up, clog the drains, and cause backflow into the house and leaks outside of the designated drain field. You should get your system checked every 3-5 years.
  • If you can convert your septic tank to a sewage line, we recommend you do so. There are funds with the Escambia County Health Department for qualified families to do this.


Though Enterococcus can come from any bird or mammal, it is assumed such high levels are due to human waste in the water. There are sampling methods now available that can confirm this.


Reports of large Harmful Algal Blooms (HABs) are not common in the bay system. The Florida Department of Environmental Protection (FDEP) monitors these statewide and reports weekly. Most are occurring in, and around, the Lake Okeechobee area and the Indian River Lagoon. Escambia County’s Marine Resource Division, and volunteers at Navarre Beach, monitor for red tide events each week. Though these are, again, a big problem in south Florida, they are not common here. Sea Grant hopes to begin a Phytoplankton Monitoring Network citizen science program in 2021 that will focus on HABs inside the bay. There are no plans yet, we are waiting on state training, but we do hope this will happen.


In 2016, an U.S. Environmental Protection Agency (EPA) publication on the environmental quality of the Pensacola Bay System came out. Entitled Environmental Quality of the Pensacola Bay System: Retrospective Review for Future Resource Management and Rehabilitation it reviews numerous published papers on different environmental parameters in the bay area – including water quality.


It mentions that most of the studies conducted were short term monitoring or sampling projects. The longest long term monitoring has been conducted by the Bream Fishermen’s Association (BFA) – They have been monitoring nutrients and bacteria since 1968. The publication mentions that though all three rivers are in good shape, Blackwater was in better shape than the Yellow and Escambia. There have been numerous reports of hypoxia in the bay area but reminds everyone that these can be caused by natural processes as well. There have been reports of algal blooms, particularly in Escambia Bay, but these have not been harmful algal blooms. Nutrients have been reported as low to eutrophic (high) and most chlorophyll a readings have been “good” (based on federal and state criteria). However, nutrients and chlorophyll are higher in Escambia and East Bays than the other locations. And even though some of these (such as Escambia Bay and Bayou Chico) are listed as impaired due to nutrient concentrations, the symptoms of eutrophication (fish kills) have not been happening.


Fewer studies have been conducted on trace metals (such as arsenic, copper, and mercury) and persistent non-nutrient organics (such as pesticides, and PCBs). Trace metals have been tracked in the water column (where chromium, zinc, and lead have been found), surface sediments (arsenic, zinc, chromium), periphyton – microscopic algae found on rocks, shells, and seagrass (zinc), oysters – both caged and wild harvest (zinc), seagrass (zinc), blue crab (zinc), and mussels (also zinc). Other trace metals have been found in these as well and the complete list can be found in the EPA document at the link below.


Pesticides and PCBs have also been found but are usually below the threshold developed by the federal and state agencies.


You can read more about these water quality issues and their concentrations in the EPA document at the link below.


Posted: February 8, 2021

Category: Coasts & Marine, Natural Resources, Water
Tags: Florida Sea Grant, Water Quality

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