http://sanctuaries.noaa.gov

Phytoplankton Blooms in Florida Bay

Florida Bay Algae Blooms Cause Widespread Concern 

Marine, estuarine and fresh bodies of water sometimes experience phytoplankton or algae blooms. Blooms are sudden population 

explosions of microalgae or blue-green bacteria living in the water column. The phytoplankton blooms observed in Florida Bay in the 

early 1990s were highly visible, publicized events that drew concern from anglers, citizens, resource managers and scientists. 

Pea-green soupy bloom water developed in the north central bay 

at about the same time as the unprecedented die-off of many 

acres of seagrass in the area. Loss of turtle grass (Thalassia 

testudinum) habitat meant the loss of important nursery grounds 

for fish and other invertebrates. Shortly thereafter, bloom waters 

flowed southward, settling over hardbottom communities, where 

they contributed to the death of loggerhead sponges, a favorite 

hiding place for commercially valuable spiny lobsters. Almost 

immediately, it seemed important to know more about the cause 

of the blooms and possible impacts on Florida Bay’s ecology. 

Scientists from nearby academic institutions and government 

agencies launched studies to learn about the conditions that 

led to the blooms and their effects on the ecosystem. They 

soon determined that the bloom in the north central bay was 

caused primarily by a species of cyanobacteria, Synechococcus 

elongatus. Cyanobacteria, also called blue-green bacteria, are among the hardiest and oldest organisms on Earth. They date back 

in the fossil record 2.8 million years and differ from microalgae in that they are only a fraction of the size and have a much simpler 

cell structure. 

Seagrass Die-off and Drought Conditions Fueled Blooms

The conditions that triggered the north central bay blooms in the 

early 1990s have been difficult to assess, but scientific studies 

and long-term monitoring results have helped unravel much of the 

mystery. In the late 1980s, when many acres of turtle grass in 

the north central bay died simultaneously, large amounts of 

nutrients were released into the water column upon decomposition. 

Scientists now know that decomposing seagrass was one nutrient 

source fueling the bloom. Another source was the organic matter 

trapped in the sediments beneath the seagrass plants on the seafloor. 

When the plants died, these sediments floated up from the bottom, releasing the nutrient-rich organic matter into the water column. 

Once dissolved in the water column, the nutrients could be used by 

cyanobacteria for growth, thus compounding the bloom and further stressing the seagrass by reducing the sunlight reaching them. 

Florida Keys National Marine Sanctuary

http://floridakeys.noaa.gov/

A microscopic view of a cyanobacteria, S. elongatus. Photo: Florida Fish and Wildlife Conservation Commision

A dying sponge in bloom water in Florida Bay in the early 1990s.

Photo: Florida Fish and Wildlife Conservation Commission
To learn more about these and other accomplishments, 

visit sanctuaries.noaa.gov

S. elongatus Thrives in High Salinities

During the late 1980s, South Florida had been 

experiencing drought conditions, which drove Florida Bay salt 

levels (salinities) much higher than usual--even twice that 

of oceanic seawater. Unlike most phytoplankton species, 

S. elongatus was able to thrive in these extreme conditions. 

This unusually competitive species flourishes in low light 

conditions and very high salinities. In many instances, lack 

of phosphorus limits phytoplankton growth, but this species 

has a superior ability to compete for even small amounts of 

phosphorus. S. elongatus can also regulate its buoyancy, 

allowing it to take advantage of nutrients released from 

the sediments near the seafloor. The bloom observed in 

southern Florida Bay beginning in 2007 is reminiscent of the 

earlier blooms and is also largely caused by S. elongatus. 

Western Bay Blooms Caused by Different Species

Waters in western Florida Bay also experienced 

phytoplankton blooms throughout the 1990s. Western Bay 

blooms were caused by species of diatoms—microalgae that contain yellow-brown pigments and have thin, glass-like shells. Diatom populations in western Florida Bay experience blooms under the right combination of nitrogen, phosphorus and silicon, a 

mineral needed to grow the diatom shell. The onset of the western bay diatom blooms appeared to be related to the input of river 

water from land-based sources, especially from Shark River Slough on Florida’s southwestern coast, and from the long-shore current that moves water along the coast south toward Florida Bay. 

Blooms Can Flow from the Bay to the Reefs

Blooms have also been observed flowing through the passes between the Keys from the bayside to the ocean side, where they 

may cover nearshore reefs for varying periods of time. Generally, the turbid conditions produced by blooms are not favorable 

for corals and other marine animals that thrive in relatively clear, low-nutrient waters. Aerial observations of the blooms in the 

1990s showed that when blooms reached the ocean side, they sometimes dissipated relatively quickly. At other times, bloom 

waters were carried north with the Florida Current or south with the long-shore current before breaking apart. 

Scientists Monitor Water Quality and Blooms

Much of what is known about blooms has been 

learned from monitoring water quality and 

conducting experiments on bloom species. Florida 

International University scientists have been 

tracking phytoplankton blooms and water quality in 

Florida Bay, the Florida Keys National Marine 

Sanctuary and adjacent waters for many years. They 

collect monthly data about water temperature, 

salinity, turbidity, nutrients and the concentration of 

chlorophyll-a, a plant pigment that provides an 

estimate of the density of phytoplankton blooms. Water 

quality reports, including chlorophyll-a maps, are 

available at http://serc.fiu.edu/wqmnetwork. Funding for this monitoring has been provided by the U.S. 

Environmental Protection Agency (EPA) through the 

Water Quality Protection Program for the Florida Keys 

National Marine Sanctuary and by other agencies. 

Written by: Nancy Diersing, Florida Keys National Marine Sanctuary

Published: May 2009 

Bloom water in Florida Bay is green on this satellite image taken in 2007.

Photo: MODIS Land Rapid Response Team

The Florida reef tract is located on the ocean side of the Florida Keys. 

Photo: Florida Keys National Marine Sanctuary