Recent studies have shown that the fecal indicator bacteria (FIB) currently used to indicate water quality in the coastal environment may be inadequate to reflect human viral contamination. Coliphage was suggested as a better indicator of human viral pollution and was proposed by the U.S. EPA as an alternative indicator for fecal pollution in groundwater. In this study, we investigated the occurrence and distribution of FIB, F؉ coliphage, and PCRdetectable human adenovirus and enterovirus for an entire year at 15 locations around the Newport Bay watershed, an important southern California estuary for water recreation and an ecological reserve. Peak concentrations and prevalences of FIB and F؉ coliphage were associated with winter storms (wet weather). Human adenoviruses and enteroviruses, however, were detected by PCR in ϳ5% of samples collected in the summer (dry weather) but only once in wet weather. These results demonstrated that FIB and coliphage have similar seasonal and freshwater-tosaltwater distribution patterns, while the detection of human viruses depends on a distribution pattern that is the opposite of that of FIB and coliphage. This research suggested that coliphage and FIB share similar environmental sources, while sources of human viruses in Newport Bay are perhaps different.Coastal recreational water quality standards in California and throughout most of the world are based on the concentration of coliforms or Enterococcus spp., known as fecal indicator bacteria (FIB). However, the adequacy of current water quality standards to indicate the presence of human viral pathogens is still questionable. For example, Marino et al. (23) conducted a study of two Mediterranean bathing beaches, using WHO/UNEP and European Community bathing water directives as the microbial water quality guidelines. They concluded that neither set of guidelines was successful for protecting the public from health hazards related to fecal contamination of bathing water (23).