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The effect of three different liquid manure treatments on irrigated crop nutrient uptake, crop yield, soil water quality, and groundwater quality are investigated for a typical California dairy. Animals are housed in open feedlot barns surrounded by exercise yards (corrals). Flush lanes are used to remove manure, from which solids are separated and sold off-farm. The liquid manure is stored in ponds (lagoons) and applied through the existing irrigation system on forage crops. We contrast conventional manure application practices, which largely ignore the nutrient value of the manure, with targeted manure applications designed to fully replace commercial fertilizer applications and to match the crop nutrient uptake. The targeted manure applications are split into two treatments, one that accounts only for the ammonia-N in the manure, and a second treatment that accounts for both ammonia and organic nitrogen. The three treatments are implemented sequentially in the same two fields over a seven year period. The fields have a loamy sand soil and are border flood irrigated. Shallow groundwater quality monitoring at and immediately below the water table occurred almost continuously throughout the seven year period. Growers records are used to describe the timing and approximate amount of manure applications and crop management during the conventional treatment period. Detailed crop nutrient uptake, irrigation flow, manure nutrient, and soil nutrient concentration measurements are made at each irrigation during the three year period of targeted manure management. Conventional treatments resulted in elevated nitrate-nitrogen concentration at the water table, averaging approximately 100 mg/l. With targeted manure management, nitrate-nitrogen concentrations at and immediately below the water table were reduced by over 50% in the first two years of targeted manure management. Balancing the nutrient application by also accounting for the organic nitrogen in the manure application further reduced the nitrate levels in shallow groundwater. We show that a detailed field nitrogen balance coupled with a simplified site-specific groundwater model provides a practical tool to predict the impact of these treatments on shallow groundwater quality.