Excessive levels of fecal indicator bacteria are a major cause of water quality impairment. Grazing and its management may significantly impact bacteria concentrations; however, other sources can contribute to water quality issues both in the presence and absence of cattle, thus confounding results. In this study, we utilize Bacteroides markers to evaluate bacteria loading from cattle versus background sources in runoff from rotationally grazed and ungrazed pastures and how grazing management, timing of runoff in relation to grazing events, and stocking rate affect Bacteroides marker (AllBac and BoBac) levels and ratios and their relation to E. coli concentrations in runoff at the small watershed scale. The data suggest that the AllBac and BoBac levels were not significantly impacted by grazing management or stocking rate; however, the timing of runoff events in relation to grazing events significantly impacted the levels of these markers found in runoff. Furthermore, the BoBac/AllBac ratio confirmed that fecal contamination present in runoff when sites were destocked for over two weeks largely originated from sources other than cattle. Thus, the magnitude and proportion of cattle impacts on fecal indicator bacteria in edge-of-field runoff were dramatically reduced shortly after de-stocking. However, background sources continued to contribute significant concentrations of E. coli.