For over a year, water samples form five sites in and around Elkhorn Slough, and six sites in and around the Tijuana River reserve were tested for the presence of total and fecal coliforms and the anaerobic bacterium, Bacteriodes vulgatus.  Previous research in our laboratory indicated that the anaerobic bacterium could potentially serve as an alternative indicator for human fecal contamination in shellfish and estuarine waters. A new selective medium developed in our laboratory was utilized to detect Bacteroides vulgatus. The data indicate that high coliform counts did not correlate with the presence of the test bacterium in water samples: however a variety of other anaerobic bacteria were detected, especially in samples known to be associated with animal fecal contamination. These data indicate that the test bacterium, Bacteroides vulgatus, is more human specific than other members of the Bacteroides fragilis group, and may be a better indicator for human fecal contamination than the coliforms. The highest coliform counts were observed during rainfall events and were probably due with overgrowth of coliforms in the environment due to animal contamination.