Restoring the Health of Pensacola Bay, what can you do to help? Biodiversity

Records of the variety of aquatic life in Pensacola Bay go back to the 18th century. According to these reports, over 1400 species of plants and animals call Pensacola Bay home. Many of them depend on seagrass, oyster reefs, or marshes to complete their life cycle. The greatest diversity and abundance are found on the oyster reefs. Finfish and shellfish in the bay have sustained humans as a food source for centuries. However, we know that the alligator, turtles, and a variety of birds and mammals have also been important. In this article, we will focus on the aquatic species.

An icon of northern Gulf coast commercial fishing – shrimping.
Photo: NOAA

When people think of aquatic life in the bay, they first think of fish. About 200 species call Pensacola Bay home. The most abundant are the true estuarine fish, such as croakers, sardines, and minnows. There are a variety of marine transient fish that can be found such as jacks, mackerels, and some species of sharks. Spot and Atlantic Croaker are the most abundant members of the croaker family, and are still an important target fish for locals. Anyone who has snorkeled or cast a line with cut bait knows how common pinfish can be, and those who have pulled bait nets are very familiar with the silverside minnows and anchovies.


I have pulled many a seine net over the years assessing the diversity and abundance of the nearshore fish populations and logged 101 species. In addition to those listed above, killifish (also locally known as “bull minnows”) are a common capture. For a few years, we were involved in trawling in deeper waters where we collected a variety of flounder, silver perch, grunts and snapper. Sea robins are an interesting member of our community and gag grouper were captured occasionally. The number and variety of fish found varies with seasons and is greatest in June. The diversity and abundance of estuarine fishes in our bay is very similar to neighboring estuaries.


The second thing people think of when they think of aquatic life in the bay are shellfish. These would include the crabs, shrimp, and oysters. However, the most abundant macro-invertebrates in our bay are those that can tolerate environmental stress and live in the surface layers of the sediments – these are the worms and crustaceans. There are numerous varieties of segmented polychaete worms, who are famous for building tunnels with “volcano” openings. They are also common within oyster reefs, feeding on all sorts of organic debris. Blue crab are common throughout the bay and provided both a commercial and recreational fishery for years. Brown and white shrimp are both found and have been the most popular seafood with locals for years.

The magnificent blue crab.
Photo: Molly O’Connor

During my lifetime, the only marine mammal commonly seen has been the Atlantic Bottlenose Dolphin, and these are found in many parts of the bay. Years back, I heard accounts of harbor porpoise, but never actually saw one. An historic occurring marine mammal, who seems to be making a comeback, is the Florida Manatee. Sightings of this animal have been reported in a variety of locations in recent years.


Snakes, turtles, and alligators are all found in the bay area. There is really only one saline snake and this is the gulf coast salt marsh snake. However, nontraditional estuarine snakes, such as the cottonmouth, are becoming more common in and near the bay. Though we have a great variety of turtles in our rivers, only one true estuarine turtle exist in the country, the diamondback terrapin – and this turtle can be found in parts of our bay. Sea turtles do venture into the bay searching for food, particularly the green turtle who is fond of seagrasses.

Gulf Coast Salt Marsh Snake
Photo: Molly O’Connor

Many forget the small planktonic animals that drift in the water column, but they are there – about 100 species of them. Copepods are small roach looking crustaceans that are by far the most abundant member of the zooplankton, particularly the species known as Acartia tonsa – which makes up 82% of the abundance in our bay. These small animals are an important link in the food chain of almost every other member of the bay community. The zooplankton variety in Pensacola Bay is very similar to those of neighboring estuaries.


And then there are the plants…

By far, the most diverse group of organisms in the bay are the microscopic plants known as phytoplankton – with over 400 species reported. Much of the bay is too deep to support traditional forms of plants and so these become a key producer of food for many species. The diversity and abundance is greatest in the spring and fall. 70% of the phytoplankton are from a group called dinoflagellates, small plants that have two hair-like flagella to orient, and even propel, themselves. Some of them produce the bioluminescence we sometimes see and others produce what we call red tide. During the summer, the populations change and the more abundant forms are diatoms. These lack the flagella of the dinoflagellates, but they do produce beautiful shells of silica.


There are at least 400 species of periphytic algae (attaching). Green algae are the most abundant and are most common in the local bayous. Cyanobacteria, which were once thought to be algae, are the most abundant in the marshes and periphytic diatoms dominate in the Sound.

The seagrass commonly known as Shoal Grass.
Photo: Leroy Creswell

And last, are the submergent and emergent grasses.

Submergent grasses are known as seagrasses. We have three species that like the higher saline waters. These are turtle, shoal, and widgeon grass. Turtle and shoal grass need the water to be at least 25 parts per thousand and are the dominate species in the lower portions of the bay. Widgeon grass can tolerate waters as low as 10 ppt and are found in the bayous and the upper portions of the bay system. Tapegrass only survives in freshwater and are found in the lower reaches of the rivers where they meet the bay.

Emergent grasses are what we call marsh grasses. Two species, Black Needlerush and Smooth Cordgrass dominate these. There are pockets of salt marshes found all over the bay system.


So how is the health of our aquatic life?

As you might expect, the diversity and abundance have declined over time, particularly since the 1950’s. One firsthand account of the change, describe a bayou that was clear, full of grass, and harbored shrimp the size of your hand. Then they were gone. He remembered the first change being water clarity. As development along our waterfront increased, the clarity decreased and the aquatic life declined. This has happened all over the bay system. Increase in run-off not only brought sand and sediment lowering water clarity, it also brought chemicals that both the plants and animals could not tolerate. Much of the point source pollution has been controlled but non-point pollution is still problematic. Fertilizers, pesticides and herbicides, oils and grease, and sediment have all been problematic. These can be reduced. Following recommendations from the Florida Friendly Landscaping website, ( property owners can alter how they are currently managing their landscape to reduce their impact on the aquatic life on the bay. Clean Marina ( ) and Clean Boater ( ) recommendations can help reduce the impact from the boating community. Sustainable fishing practices, such as safe catch and release methods for unwanted fish and removing all monofilament are good practices. In 2019, Sea Grant will begin a program training local citizens how to monitor the diversity and abundance of aquatic species. If interested in volunteering, stay tuned.




Lewis, M.J., J.T. Kirschenfeld, T. Goodhart. 2016. Environmental Quality of the Pensacola Bay System: Retrospective Review for Future Resource Management and Rehabilitation. U.S. Environmental Protection Agency. Gulf Breeze FL. EPA/600/R-16/169.


Posted: May 12, 2018

Category: Coasts & Marine, Natural Resources
Tags: Estuaries

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