Controlled subsurface drainage irrigation systems promote crop productivity; however, these land management systems also allow an efficient pathway for the transport of elements from soils to surface water resources. The nitrate and macro-element effluent concentrations from tile-drainage involving a 40 ha controlled subsurface drainage irrigation system are described and compared to soil nitrate availability. Soil nitrate concentrations generally show an increase immediately after soil nitrogen fertilization practices and are sufficiently abundant to promote their transport from the soil resource to the tile-drain effluent waters. The data indicates that: (1) the transport of nitrate-N in tile-drain effluent waters is appreciable; (2) denitrification pathways effectively reduce a portion of the soil nitrate-N when the controlled drainage system establishes winter-early spring anoxic soil conditions, and (3) the best strategy for reducing nitrate-N concentrations in tile-drain effluent waters is adjusting N fertilization rates and the timing of their application. The development of bioreactors for simulating wetland conditions may further limit nitrate concentrations in surface waters because of soil drainage.