This survey provides information on sediment toxicity and structural characteristics of the macrobenthic and periphytic algal communities at 10 locations in northeast Florida Bay. Whole sediments were not acutely toxic to Mysidopsis bahia (marine invertebrate) and Hyalella azteca (freshwater invertebrate) relative to reference sediment. Survival was between 80% and 100%. Community structure of the macrobenthos and algal-periphyton varied spatially. A total of 116 benthic species were identified at the 10 locations; mean density was greater in Shell Creek (10,017 organisms/m2) and least in Canal C-103 (441 organisms/m2). Tubificids and the crustacean Halmyrapseudes bahamensis (Family: Apseudidae) dominated the benthos at 4 of 10 locations. One hundred and six species of periphytic algae representing 52 genera were identified on substrates colonized for 21 days. Mean algal density was greater in Florida Bay (19,440 cells/cm2) and least in Long Sound (10 cells/cm2). Diatoms and blue green algae dominated the algal-periphyton. Major diatom genera were Navicula, Brachysira and Nitzschia. The more abundant and widely occurring blue-green taxa were species of Oscillatoria, Polycystis and Lyngbya. Ash free dry weight and chlorophyll a were significantly greater for periphyton colonized in Canal C-111 and Florida Bay and the least in Long Sound. Spatial variation and the availability of reference areas are important issues that need consideration in future biomonitoring efforts conducted in this region to ensure relevancy of results.