Hypoxia is a year-round phenomenon in Pensacola Bay with dramatically higher frequency and extent from June through October, affecting 24 percent of the bay bottom. It is one of the most important water quality issues in the system. The other major concern is the fact that submerged aquatic vegetation (SAV) distribution decreased by about 50 percent between the 1960s and 1980 and still remains low.
A substantial portion of the estuary is usually well-stratified at a depth of 1–2 meters. Bottom salinity can be up to 20 times higher than surface salinity. The location of hypoxic waters is strongly associated with water column stratification. Metabolic rates are relatively low in bottom waters, indicating that the system is extremely sensitive to developing hypoxia, but not as a result of high DO demand. The condition of benthic macrofaunal communities as a result of hypoxia is not characterized at this time.
Nutrient loading of Pensacola Bay is moderate and phytoplankton production and biomass are relatively low compared to other estuaries. Consequently, water clarity and nutrient concentrations are generally favorable to SAV growth, but the population has not responded. Metabolic stress associated with high sulfide in sediment pore waters has been implicated as a possible cause for the lack of new SAV growth.
Pensacola Bay system is a complex of estuaries that Escambia Bay, Blackwater Bay, East Bay, and Pensacola Bay propoer. There are relativity few ecological studies and no attempt made to document the differences for classification purposes. There is a salinity gradient from Escambia River seaward to Pensacola Pass and nutrient levels decrease along the gradient that might be used for spatial classification.
The data record begins with an ecological survey conducted in 1975, but no other comparable data were collected until EPA began conducting surveys in 1996. Comparisons of data indicate that conditions did not change dramatically during the gap years. More information is needed to better understand the causes of the impaired condition of SAV beds (National Estuarine Experts Workgroup 2010).
Reference:
National Estuarine Experts Workgroup. 2010. Nutrients in Estuaries: A Summary Report of the National Estuarine Experts Workgroup 2005–2007. U.S. Environmental Protection Agency. Accessed October 2016. https://www.epa.gov/sites/production/files/documents/nutrients-in-estuaries-november-2010.pdf.