Long-term nitrate leaching data from four annual corn-soybean-wheat row-crop systems and two perrenial systems (alfalfa and poplar trees) in southwest Michigan. Leachate concentrations were collected using quartz suction lysimeters and analyzed for nitrate and ammonium concentrations. Nitrate flux was calculated using simulations of water movement through the profile using the SALUS crop model. Systems were analyzed for total nitrate leaching throughout an entire rotation, as well as for leaching differences within the rotation. Our organic system leached significantly less nitrate than conventional systems. However, all row-crop systems showed a greater flux of nitrate during the period between corn and soybeans than at any other time during the rotation. Alfalfa showed nitrate losses that were similar to the conventional systems, while the poplar trees showed much lower losses.