For over a century, specific types of bacteria have been monitored in natural water bodies as indicators of fecal pollution and increased risk of encountering human pathogens. One such type of bacteria is the fecal coliforms, a group of gram-negative, facultative anaerobes mostly from the Class Gammaproteobacteria and the Family Enterobacteriaceae, which are commonly found in the gut of warm-blooded animals. In the Chesapeake Bay, routine monitoring of coliform bacteria has been conducted since the 1920’s to assess the likelihood of sewage pollution in shellfish harvest areas. The research for this dissertation examined the dynamics and drivers of fecal coliforms and potential pathogen groups in Maryland waters. First, the impacts of climate variability on densities of fecal coliforms in surface waters were examined, finding that annual precipitation and air temperature levels correlate well to the proportion of stations with fecal coliforms in excess of the established regulatory criteria. A dominant climate pattern was identified for years with extreme precipitation and fecal coliform levels. Secondly, the validity of using precipitation totals as indicators of fecal coliform densities exceeding the regulatory criteria was examined. Precipitation levels over the previous two days were related to fecal coliforms in excess of the criteria for particular watersheds, depending on the percent of open water; non-tidal, forested wetlands; and soil types. The level of precipitation required to cause fecal coliform densities to exceed the FDA criterion varied between watersheds. Thirdly, high-throughput sequencing of 16S rRNA genes was used to study the community of bacteria at a long-term monitoring station in order to characterize community members over the course of 5 months. Water temperature and turbidity were found to be related to changes in community composition at the scale of Genera, while precipitation was a key driver for the presence of allochthonous bacteria such as fecal coliforms. The co-occurrence of some bacteria groups at the Class level of phylogeny was largely defined by the arrival of allochthonous groups into the autochthonous community. Further, a novel approach for estimating densities of bacteria from 16S rRNA amplicon pools was explored.