The microbiology of stream water has a seasonal component that results from both biogeochemical and anthropogenic processes. Analysis of nonevent conditions in streams entering Conesus Lake, NY (USA), indicated that total coliform, Escherichia coli, and Enterococcus spp. levels peak in the summer in all streams, independent of the agricultural use in the stream sub-watershed. Prior to implementation of management practices, E. coli in water draining Graywood Gully, a sub-watershed with 74% of the land in agriculture, reached as high as 2806 CFU/100 mL, exceeding the 235 CFU/100 mL EPA Designated Bathing Beach Standard (EPA-DBBS). In contrast, North McMillan Creek, a sub-watershed with <13% of its land in agriculture, had E. coli maxima generally near or below the EPA-DBBS. Graywood Gully at times had a higher microbial loading than North McMillan Creek, a sub-watershed 48 times larger in surface area. Over a 5-year study period, there was a major decrease in bacterial loading during nonevent conditions at Graywood Gully, especially after manure management practices were implemented, while bacterial loading was constant or increased in streams draining three other sub-watersheds. E. coli levels dropped more than 10 fold to levels well below the EPA-DBBS while the yearly maximum for Enterococcus dropped by a factor 2.5. Similarly, exceedency curves for both E. coli and Enterococcus also showed improvement since there were fewer days during which minimum standards were exceeded. Even so, Graywood Gully at times continued to be a major contributor of E. coli to Conesus Lake. If wildlife represents a significant source of indicator bacteria to Graywood Gully as has been reported, stream remediation, management efforts and compliance criteria will need to be adjusted accordingly.