Dairy and livestock grazing operations can introduce pollutants such as fecal coliform to surface waters, posing risk to human health and ecological conditions. Agricultural best management practices (BMPs) that increase control of manure, runoff, and animal access to waterways can reduce deposition of microbial pollution into streams. Between 2000 and 2013, we monitored water quality (fecal indicator bacteria [FIB] consisting of fecal coliform [FC] and Escherichia coli [EC]) in three coastal watersheds that encompass intensively managed dairies, beef cattle grazing operations, and public use at Point Reyes National Seashore in Marin County, California. Concurrently, approximately 30 BMPs were implemented to manage cattle and improve dairy infrastructure. We also monitored a fourth adjacent watershed without any BMPs and limited direct livestock influence. The primary FIB parameter was changed from FC to EC midway through the study in 2007, so we combined FC data from 2000 to 2006 with EC data from 2007 to 2013 using previously published EC/FC ratios and data from this study to create a continuous time series. Competing Bayesian generalized linear mixed models examined whether FIB was best explained by year, 24-h rainfall, season, or annual rainfall and compared results with numeric regulatory objectives for surface waters. FIB from 2000 to 2013 declined at all 13 water quality stations that were downstream of BMPs implemented during the study, while there was a slight positive trend in the adjacent watershed without BMPs and limited livestock influence. There was a 54–99% reduction in FIB with a sixfold increase in the frequency of samples meeting regulatory criteria over the study period, and results were robust to varying assumptions of the relationship between FC and EC. These findings indicate that targeted BMPs can effectively reduce FIB, increasing the probability of meeting water quality objectives across varying types of livestock operations.