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Agricultural fields, subsurface drainage, and a network of modified headwater systems dominate the landscape in the Midwest region of the United States. These systems are often the main conduits that export sediment and nutrients downstream, but very little is known about how these systems function. While most agricultural Best Management Practices (BMPs) focus on landscape measures to reduce sediment loss and water pollution little research has been performed on in-stream processes and channel system floodplains as agricultural BMPs. An important step in quantifying nutrient reduction capacities on floodplains is to predict discharges occurring on floodplains. This paper evaluates methods to predict the recurrence interval of discharges at ungaged sites and the annual exceedances of different discharge thresholds. Also presented is a study to evaluate the benefits of modifying channels to two-stage geometries that provide connection to floodplains and more bank storage. Preliminary results indicate that benches (small floodplains) should be located at elevations associated with about 25-35% of the 2-year discharge and they will usually flood about 10-60 days annually. Nitrate-N removal, in systems with flooded width ratios of 4 to 5 times the bankfull width, might be 5-20% of exports from fields if the treatment area (surface of the benches and inset channel) is about 1% of the watershed area. Results of this study are being used to develop a tool that quantifies the reduction in nitrate exports associated with different floodplain geometries and linear extent of the floodplains.