The article describes challenges in managing water resources to effectively balance the benefits and costs, including associated ecosystem services (ES) from sustainable agriculture. Methods are presented in the Middle Alabama watershed case study to evaluate ES in terms of how irrigated versus rainfed fields will affect sediment retention, fertilizer usage and the effect of the subsequent discharges of sediment and nitrogen from fertilizer on water quality. https://www.mdpi.com/2073-445X/11/12/2316.