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The Nebraska Management Systems Evaluation Area (MSEA) water quality project was a part of a multi-agency, multi-state project designed to provide a better understanding of the effects on water quality of farming systems and nitrogen inputs to crop production. Most of the Nebraska MSEA was focused on production of irrigated corn and soybean in the Central Platte Valley, where the shallow groundwater used for irrigation is highly contaminated with nitrate-N. This paper summarizes results from four studies conducted under this project. Groundwater quality response to management: Nitrate-N concentration was measured over a six-year period in leachate leaving the root zone and in groundwater beneath three fields planted to corn and irrigated with either conventional furrow irrigation, surge flow irrigation or center-pivot sprinkler irrigation. Pivot irrigation together with N applications programed according to plant need was the only management system providing groundwater quality improvement. Fertigation through surge irrigation: The distribution of N applied by fertigation through surge irrigation was too non-uniform for this practice to be recommended on the soils of the Central Platte Valley. Irrigation with high-nitrate groundwater: Furrow irrigating corn with groundwater containing 30 mg/L of nitrate-N produced maximum grain yield (12.5 - 13.2 Mg/ha) with 80 - 90 kg/ha of N fertilizer. At this yield level, fertilizer N applications of less than 160 kg/ha probably resulted in a net removal of N from the combined soil-groundwater system. N leaching loss under monoculture corn and corn-soybean rotation: Long-term field plot and lysimeter studies showed that total nitrate-N leaching loss from a corn-soybean rotation can be equal to or greater than the loss from monoculture corn if N fertilizer amounts are not reduced sufficiently during corn production to take full advantage of the residual N following soybean. In a semi-arid climate, residual N from soybean may be substantially greater than in more humid regions.