A survey of storm runoff fecal coliform bacteria (FCB) from working farm and ranch pastures is presented in conjunction with a survey of FCB in manure management systems (MMS). The cross-sectional survey of pasture runoff was conducted on 34 pastures on five different dairies over 2 yr under varying conditions of precipitation, slope, manure management, and use of conservation practices such as vegetative filter strips. The MMS cross-sectional survey consisted of samples collected during 1 yr on nine different dairies from six loafing barns, nine primary lagoons, 12 secondary lagoons, and six irrigation sample points. Pasture runoff samples were additionally analyzed for Cryptosporidium sp. and Giardia duodenalis, whereby detectable concentrations occurred sporadically at higher FCB concentrations resulting in poor correlations with FCB. Prevalence of both parasites was lower relative to high-use areas studied simultaneously on these same farms. Application of manure to pastures more than 2 wk in advance of storm-associated runoff was related to a > or =80% reduction in FCB concentration and load compared to applications within 2 wk before a runoff event. For every 10 m of buffer length, a 24% reduction in FCB concentration was documented. A one-half (75%), one (90%), and two (99%) log10 reduction in manure FCB concentration was observed for manure holding times in MMS of approximately 20, 66, and 133 d, respectively. These results suggest that there are several management and conservation practices for working farms that may result in reduced FCB fluxes from agricultural operations.