Non-point source contamination is a major water quality concern in the upper Midwestern USA, where plant nutrients, especially NO3-N, are susceptible to leaching due to extensive subsurface draining of the highly productive, but poorly drained, soils found in this region. Environmental impacts associated with intensive mineral fertilization in conventional production have encouraged producers to investigate organic methods. The USDA-ARS Organic Water Quality (OWQ) experiment, established in 2011, compares organic (C-S-O/A-A) and conventional (C-S) crop rotations and an organic pasture (bromegrass, fescue, alfalfa, white clover) system. Thirty fully-instrumented, subsurface-drained plots (30.5 m × 30.5 m) laid out in a randomized block design with 5 field replications, isolate subsurface drainage from each plot and permit comparison of treatment effects on subsurface drainage water flow and nutrient concentrations. Objectives for this study were to quantify growing season subsurface drainage water flow, NO3-N concentrations, and NO3-N loads for conventional and organic grain cropping systems from 2012-2014. Temporal patterns of subsurface drainage water flux were similar for all cropping systems for all years, except for the pasture system in 2012 and subsurface drainage water N concentrations were highest in the conventional C-S system except for the early spring 2012. Subsurface drainage water N loading loss for the entire 3-year period from the conventional C-S system (79.2 kgN ha-1) was nearly twice as much as the N loss from the organic C-S-O/A-A system (39.9 kgN ha-1); the pasture system (16.5 kgN ha-1) lost the least amount of N over the 3 years. Results of this study suggest that organic farming practices, such as the application of composted animal manure and the use of forage legumes and green manures within extended cropping rotations, can improve water quality in Midwestern subsurface-drained landscapes.