To characterize the quality of sediments at key sites in the Galveston Bay Estuary, sediment samples were collected concurrently for chemical and physical analyses, toxicity testing and an assessment of benthic community structure. Significant toxicity, as determined by the sea urchin (Arbacia punetulata) pore water embryological development assay, was observed at 12 of the 24 sites investigated in this study. No toxicity was observed at any of the sites with the amphipod (Grandidierella japonica) solid-phase test. There were a number of sites with elevated levels of trace metals and petroleum hydrocarbons. The chemistry, toxicity and benthic data were ranked by station and a scaled rank sum was calculated to facilitate comparisons among the stations. Five sites exhibited strong evidence of contaminant-induced degradation, while 15 stations showed no evidence of contaminant-induced degradation. At eight additional sites the sediment quality triad (SQT) data indicated that unmeasured chemicals or conditions were stressing the system. Contaminant impacts could be reduced or eliminated by alternative regulatory and management practices, including the restriction of produced water discharges into coastal estuaries and the use of dredge material disposal practices that minimize the reintroduction of sediment-associated contaminants to the bays.