Thirty sites were sampled in southern Biscayne Bay and Manatee Bay in December 1999 to determine the extent of toxicity in sediments. Analyses and assays included: pesticides and phenols in seawater; chemical contaminants in sediment; amphipod mortality, HRGS P450, sea urchin sperm fertilization and embryology, MicrotoxTM, MutatoxTM, grass shrimp AChE and juvenile clam mortality assays; sea urchin sperm, amphipod and oyster DNA damage; and benthic community assessment. Sediment sites near the mouth of canals showed evidence of contamination. Contaminant plumes and associated toxicity do not appear to extend seaward of the mouth of the canals in an appreciable manner. Concentrations of contaminants in the sediments in open areas of Biscayne and Manatee Bays are generally low.