The ubiquity of fecal indicator bacteria such as Escherichia coli and enterococcus make tracking sources in urban watersheds extremely challenging. In this study, a multi-tiered approach was used to assess sources of fecal pollution in Ballona Creek, an urban watershed that drains to Santa Monica Bay (SMB), CA. A mass-based design at six mainstem sites and four major tributaries was used to quantify the flux of enterococcus and E. coli using traditional culture-based methods, and three additional indicators including enterococcus, Bacteroides sp. and enterovirus, using quantitative polymerase chain reaction (QPCR). Sources and concentrations of fecal indicator bacteria were ubiquitously high throughout Ballona Creek and no single tributary appeared to dominate the fecal inputs. The flux of enterococcus and E. coli averaged 109 to 1010 cells/hr and were as high at the head of watershed as they were at the mouth prior to its discharge into SMB. In contrast, the site furthest upstream had the most frequent occurrence and generally the greatest concentrations of enterovirus.