Ascertaining water quality through investigation of benthic community structure was studied. Various methods of community structure analysis, including several species diversity indexes, rarefaction curves, and a probability of interspecific encounter index, were applied to data from selected sites. Hydrographic data and sediment analysis were used in interpreting the results of the various methods of investigating community structure. The methods of investigation showed close agreement. Three of the 5 investigation sites showed normal estuarine water quality. Two other stations showed evidence of large amounts of stress, probably due to water quality; stress of one was probably due to natural causes, primarily salinity fluctuations. The other, a channel site near an industrial complex, showed intermittant stress, possibly due to man-made pollution.