If not managed properly, modern agricultural practices can alter surface and groundwater quality and drinking water resources resulting in potential negative effects on aquatic and terrestrial ecosystems. Exposure to agriculturally derived contaminant mixtures has the potential to alter habitat quality and negatively affect fish and other aquatic organisms. Implementation of conservation practices focused on improving water quality continues to increase particularly in agricultural landscapes throughout the United States. The goal of this study was to determine the consequences of land management actions on the primary drivers of contaminant mixtures in five agricultural watersheds in the Chesapeake Bay, the largest watershed of the Atlantic Seaboard in North America where fish health issues have been documented for two decades. Surface water was collected and analyzed for 301 organic contaminants to determine the benefits of implemented best management practices (BMPs) designed to reduce nutrients and sediment to streams in also reducing contaminants in surface waters. Of the contaminants measured, herbicides (atrazine, metolachlor), phytoestrogens (formononetin, genistein, equol), cholesterol and total estrogenicity (indicator of estrogenic response) were detected frequently enough to statistically compare to seasonal flow effects, landscape variables and BMP intensity. Contaminant concentrations were often positively correlated with seasonal stream flow, although the magnitude of this effect varied by contaminant across seasons and sites. Land-use and other less utilized landscape variables including biosolids, manure and pesticide application and percent phytoestrogen producing crops were inversely related with site-average contaminant concentrations. Increased BMP intensity was negatively related to contaminant concentrations indicating potential co-benefits of BMPs for contaminant reduction in the studied watersheds. The information gained from this study will help prioritize ecologically relevant contaminant mixtures for monitoring and contributes to understanding the benefits of BMPs on improving surface water quality to better manage living resources in agricultural landscapes inside and outside the Chesapeake Bay watershed.