The toxicity of sediments in Pensacola, Choctawhatchee, St. Andrew and Apalachicola Bays was determined as part of bioeffects assessments performed by NOAA's National Status and Trends Program. The objectives of the survey were to determine: (1) the spatial patterns in toxicity throughout each bay, (2) the spatial extent of toxicity throughout and among the bays, (3) the severity or degree of toxicity, and (4) the relationships between chemical contamination and toxicity. The survey was conducted over two years: Pensacola Bay and St. Andrew Bay were sampled in 1993; and Choctawhatchee Bay, Apalachicola Bay and Bayou Chico (a sub-basin of Pensacola Bay) were sampled during 1994. Surficial sediment samples were collected from 123 randomly-chosen locations throughout the five areas. Multiple toxicity tests were conducted on all samples, and chemical analyses were performed on 102 of the 123 samples. Toxicological tests were conducted to determine survival, reproductive success, morphological development, metabolic activity, and genotoxicity; all bays showed toxicity in at least some of the samples. Toxicity was most severe in Bayou Chico, an industrialized basin adjoining Pensacola Bay. Other developed bayous adjoining Pensacola Bay and the other bays also showed relatively severe toxicity. The main basins of the bays generally showed lower toxicity than the adjoining bayous. The different toxicity tests, however, indicated differences in severity, incidence, spatial patterns, and spatial extent in toxicity. The most sensitive test, a bioassay of metabolic activity of bioluminescent bacteria, indicated toxicity was pervasive throughout the entire study area. The least sensitive test, an acute bioassay performed with a benthic amphipod, indicated toxicity was restricted to a very small portion of the area. Causes of toxicity were not determined in the survey. However, mixtures of potentially toxic substances, including pesticides, petroleum constituents, trace metals, and ammonia, were associated statistically with the measures of toxicity. The concentrations of many substances were highest in Bayou Chico, where the most severe toxicity was observed. At these toxic sites, some of the substances had considerably elevated concentrations, often exceeding numerical guidelines or known toxicity thresholds. The relationships between toxicity and chemical concentrations differed among the bays and toxicity tests.