Subsurface drainage is a common water management practice in agricultural regions with seasonally high water tables. The practice of subsurface drainage provides many agronomic and environmental benefits but may also contribute substantial nitrate-N loads to surface waters. Few field studies have documented the impact of drainage intensity on nitrate-N loads in drainage waters, yet the desired drainage intensity is a critical factor in the design of drainage systems for crop production. An appropriate balance between increasing drainage intensity (narrower spacing) to improve drainage and crop yield, and decreasing drainage intensity to reduce nitrate-N losses, needs to be found for different climatic and soil regions. A long-term (20-yr) study has been conducted on a silt loam soil in southeastern Indiana, USA, to determine the impacts of drainage intensity and changes in crop production system on nitrate-N loads to drainage water. Three drainage intensities (5-, 10-, and 20-m drain spacings) are compared for drainflow characteristics, nitrate-N concentrations, and nitrate-N loads. Average drainflow per unit area is up to two times greater for the 5-m spacing compared with the 20-m spacing, which leads to proportionately greater N loads to surface waters. Although crop yield is slightly higher with the narrower spacing, nitrate-N concentrations in drainflow are not different among drain spacings. Addition of a winter cover crop as a “trap” crop for residual soil nitrate, along with lower fertilizer N rates, have significantly reduced the nitrate concentrations and loads in drainflow. Our 20-yr study on a loess-derived soil in southeastern Indiana provides an important data set for assessments of nitrate leaching into subsurface drains in the Ohio River basin. As drainage intensity continues to increase in some regions of intensive agriculture, these results underscore the importance of cover crops or other management practices to reduce nitrate-N loads even as drain water flow is increased. Additional management practices to temporarily retain or recycle some of the drained water should also be encouraged.