Over-application of manure on cropland can cause water quality degradation. This paper reports a modeling approach for assessing tradeoffs among manure storage and handling systems as they relate to the nutrient loadings in cropland runoff, including nitrate losses to groundwater. The CREAMS simulation model provided estimates of nutrient losses. A linear optimization model was used to determine the income-nutrient loss tradeoffs. Six-month storage was profitable for farmers with average-size dairy herds, but compared to daily spreading caused increased nitrate leaching through the soil to groundwater resources. Twelve-month storage systems decreased farm profitability while decreasing the total nitrogen losses from farm fields.