The objective of this work was to quantify the long-term runoff, percolation, erosion, and losses in nitrate-nitrogen, total phosphorus and pesticides attributed to multiple levels of corn stover [Zea mays L.) removal. A field-scale modeling framework, which utilized the Groundwater Loading Effects of Agricultural Management Systems/National Agricultural Pesticide Risk Analysis (GLEAMS-NAPRA) model and the Revised Universal Soil Loss Equation, Version 2 (RLJSLE2), was created and applied within Indiana to evaluate water quality impacts associated with three corn stover removal rates (38%, 52.5%, and 70%), based on proposed harvest efficiencies of three multipass field collection systems, with two tillage options (fall chisel/spring [...]