Alternative cropping systems can improve resource use efficiency, increase corn grain yield, and help in reducing negative impacts on the environment. A 6-yr (1993 to 1998) field study was conducted at the Iowa State University’s Northeastern Research Center near Nashua, Iowa, to evaluate the effects of non-traditional cropping systems [strip inter cropping (STR)-corn (Zea mays L.)/soybean (Glycine max L.)/oats (Avina sativa L.)]; alfalfa rotation (ROT)-3-yr (1993 to 1995) alfalfa (Medicago sativa L.) followed by corn in 1996, soybean in 1997, and oats in 1998), and traditional cropping system (corn after soybean (CS) and soybean after corn (SC) on the flow weighted average nitrate-nitrogen (NO3-N) concentrations and NO3-N leaching losses with subsurface drainage water. The soils at the research site are loamy with 3% to 4% organic matter and are underlain by subsurface drainage system. The data collected from four experimental treatments were analyzed as an unbalanced incomplete block design using F-test and T-test among treatments and within treatments, respectively. When averaged across 6-yr, non-traditional cropping systems reduced flow weighted average NO3-N concentrations in subsurface drain water with highly significantly effect (P < 0.01) in comparison with traditional cropping system (6.5 vs. 11.2 mg L-1). Similarly, the strip inter cropping system increased corn grain yields by 5% (9.03 vs. 8.6 Mg ha-1) and reduced NO3-N leaching losses by 6% (12.6 vs. 13.5 kg-N ha-1) and showed no difference in soybean yields when compared with traditional cropping system. Results of the study indicate that strip inter cropping and alfalfa rotation systems have the potential to reduce NO3-N leaching into the shallow groundwater system and possibly can become one of the better sustainable farming systems in Midwestern agriculture.