Transport of P, N, sediment, and pathogens from crop fields, especially where manure has been applied, can contribute to degradation of surface waters, leading to eutrophication and potential health effects. An objective of the newly established Institute for Environmentally Integrated Dairy Management (USDA-ARS,Marshfield, WI) is to assess the significance of nutrient and pathogen transport and develop improved manure and forage crop management systems for dairy farms. To meet this objective, we have established a paired-watershed field “laboratory” to monitor runoff on a landscape-scale from a site with high runoff potential (Withee silt loam, Aquic Glossudalfs). Runoff from each of four 1.5 ha field areas is monitored with a water quality station equipped with an H-flume, flow meter, and an auto-sampler for nutrients and sediment. Protozoan, bacterial, and viral pathogens are collected using a flow-through glass wool filter. All four drainage areas are currently cropped to corn harvested for silage under conventional management (manure, tillage, etc.). After a 1-to-2-year calibration period to establish a statistical relationship between drainage areas, three areas will be shifted to alternative management systems (cover crop, manure management, etc.), while one will remain as the control. Preliminary data from event-based sampling in the early calibration period will be presented.