Oysters in the Pensacola Bay system are in critical condition, while seagrass beds have leveled off but remain far below their historic extent. That’s according to the biennial "State of the Bays" report released Tuesday by the Pensacola and Perdido Bays Estuary Program. The report paints a picture of contrasts: some progress in water quality, but keystone habitats still under strain, and aging infrastructure adding new pressures.
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“Just like people need health checkups, so do our waters,” program director Matt Posner said. “The State of the Bays Report provides a snapshot of key ecosystem health metrics for the Pensacola and Perdido Bay watersheds, and serves as a centralized source of information for the community to learn more about the condition of our local waterways.”
The report compiles status‑and‑trend summaries across habitats, water quality, bacteria, and wildlife, assigning each indicator a plain‑language rating: improving, stable, declining, critical, or undetermined. It also introduces a new fisheries lens that tracks species richness, highlighting recreational and commercial species such as gray snapper, speckled trout, and brown shrimp. Posner said the findings are a mix of progress and warning signs.
“We’ve seen quite a bit of stability in some of our water quality parameters," he said, "… but there’s quite a few cautionary tales in the report as well.”
Oysters are perhaps the sharpest of those cautionary tales.
Oysters in Crisis
“Our oyster habitat continues to be in a state of critical condition in the greater Pensacola Bay system,” Posner said. “We’ve lost around 500 acres of habitat from 2010 to 2021.”
Posner noted that historically, the system has lost much more of its oyster coverage, between 90–95%, leaving no commercially viable wild harvest today. The report underscores why that matters, from both an ecological and an economic perspective.
“Oysters are sessile, filter-feeding invertebrates that create complex reef structures which provide homes for other organisms, including mussels, crabs, small fish, and shrimps,” the report says. “Oysters are a keystone species and ecosystem engineers that can also act as an environmental health indicator.”
They’re also economically valuable. Pensacola’s waters once supported a thriving oyster industry, second only to Apalachicola, which historically accounted for about 90% of the state’s wild oyster harvest.
“The other 10% came right out of Pensacola Bay and specifically East Bay and Escambia Bay," Posner said. "… (Oysters here) were known to be prized for the taste and beauty.”
Today, aquaculture businesses are keeping the local oyster name alive, but Posner stressed the need to restore reef habitat, as well.
“We’re actually working on a long‑term, 10‑year effort currently to bring back oysters in the Pensacola Bay system through our oyster restoration initiative,” he said.
Seagrass and Water Quality
Seagrass, another key habitat, shows more stability on paper. The report rates coverage in both bays as stable, meaning there has been no significant net loss in recent years. But Posner cautioned that “we are still down half or a little over half of the historic seagrass coverage that we once had.”
Seagrasses need clear water and sufficient sunlight to grow, Posner explained. Pollution and sedimentation cloud the water and block the light that grasses depend on, while in some areas, shifting sands and wave energy further complicate recovery.
Water quality tells two different stories. In the Pensacola Bay System, scientists say levels of nitrogen, phosphorus, dissolved oxygen, water clarity, and algae are all stable. In Perdido Bay, dissolved oxygen is improving, nitrogen is stable, but phosphorus and algae are trending worse, and water clarity is unknown because of gaps in monitoring. Here’s what those measures mean: nitrogen and phosphorus are like fertilizer that feed algae; algae levels are measured through chlorophyll‑a; dissolved oxygen is the supply fish and shellfish need to breathe; and water clarity — also called turbidity — is simply how clear or cloudy the water is.
Sewage and Public Health
The report also tracks bacteria advisories and sewage discharges. In the last two years, sanitary sewer overflows increased in the Pensacola Bay watershed while declining in Perdido. Records show 79 overflows in Pensacola in 2023 (roughly 1.5 million gallons) and 79 again in 2024 (about 2.2 million gallons). In Perdido, there were 45 overflows in 2023 (about 1.1 million gallons) and 52 in 2024 (about 300,000 gallons). The report explains why these events matter.
“Untreated wastewater can enter surface waters when precipitation overwhelms the drainage systems during storm events, when sewer lines become blocked, when lift stations are offline, or when the wastewater treatment plant (WTP) is operating at max capacity,” it says. “All of these instances can lead to sanitary sewer overflows, which discharge nutrients and pathogens into surface waters, potentially leading to low dissolved oxygen events and eventual ecosystem decline.”
Posner noted that the impacts of these overflows extend beyond ecology.
“That closes recreational areas for swimming," he said, "but it also closes shellfish harvesting. And there is a business impact to that.”
Public health data echo the infrastructure story. Swimming advisories were less frequent in Perdido Bay but held steady in the Pensacola system. Urban bayous — Chico, Grande, and Texar — were highlighted for frequent exceedances of bacterial standards.
The report’s new fisheries category reflects mixed conditions as well. Species richness is higher in lower Perdido Bay, where seagrass is abundant, and overall stability has been observed there. In Pensacola Bay, inconsistent monitoring means most conditions are undetermined, except for Santa Rosa Sound. Manatee sightings remain steady across both systems.
Growth Pressures
Beyond water quality and sewage issues, Posner pointed to the way suburban growth is reshaping the landscape and consuming natural habitat.
“What we’re really talking about is natural and agricultural land uses converting to development," he said. "... It’s transitioning into a medium‑intensity pattern of subdivisions. We want to see growth and a thriving economy, but what we really want to focus on is what does that sustainable growth pattern actually look like? If we want to bring back the oyster habitat coverage that we talked about earlier, we need to get some of these other policy and development situations straightened out.”
