Studies that evaluate the linkages between watershed improvement through Best Management Practices (BMPs) and downstream outcomes are few. Water quality of coastal waters is often impacted by soil and nutrient loss from watersheds in agriculture. Mitigation of these impacts is of concern in the Great Lakes, the Finger Lakes Region of New York State, and generally in water bodies of North America. In this issue, we report on hypothesis-based research at the watershed level evaluating the impact of BMPs on mitigation of nonpoint sources of nutrient and soil loss to streams and the nearshore zone of a lake. Specifically, we hypothesize not only reductions in nutrient and soil losses from watersheds but also a resultant decrease in metaphyton (filamentous algae), coliform bacteria, and macrophyte populations in the nearshore at stream mouths draining sub-watersheds where BMPs were introduced. Small experimental sub-watersheds, predominantly in agriculture (>70%), were selected to ensure that effects on downstream systems would not be confounded by other land use practices often observed in large watershed approaches. In this introductory paper, we provide background information on Conesus Lake, its watershed, and the Conesus Lake watershed project, a large multi-disciplinary study evaluating agricultural management practices. The series of papers in this volume consider the effect of BMPs designed to control nonpoint sources on water chemistry, metaphyton, macrophytes, and microbial populations in the coastal zone of a lake. Ultimately, this volume expands the basic understanding of the ability of BMPs to control nonpoint source pollution while contributing toward the goal of improving water quality of downstream systems including streams, embayments, and the nearshore of large lakes.