Human activity has dramatically altered the natural nitrogen (N) cycle by tripling annual terrestrial N2 fixation through legume cultivation and ammonia synthesis. The predominance of annual grain cropping systems leads to fallow fields between growing seasons. In the upper Midwest United States, fallow fields are prone to nitrate (NO3) loss from soils to rivers and streams. This loss occurs mainly in the spring, as warm temperatures allow microbes to convert soil N to NO3, and spring rains lead to NO3 moving out of fields as drainage or soil surface runoff. Cover crops are plants that are grown to improve or manage soil nutrients and structure instead of for harvest. In Iowa, the cold-tolerant cover crop cereal rye (Secale cereale L.) is well-suited to reduce NO3 loss by using NO and water when annual grain crops, such as corn, soybeans, or other plants grown for grain, are not growing and using NO3. However, the ability to grow cover crops is affected by the grain crop system in which they are grown. Rye must be terminated 10 days before corn (Zea mays L.) planting to maintain corn yield, but rye can be terminated any time before soybean (Glycine max L.) planting without affecting production. Since soybeans are planted on average 14 days later than corn, rye before soybeans can potentially have an average of 24 extra days to immobilize NO3, especially important at a time when most NO3 is lost. In addition to grain crop, the method of cover crop termination may also affect the ability to grow cover crops. Farmers can choose from a variety of herbicides and times at which to terminate cereal rye prior to corn or soybean planting, which may affect the potential for soil NO3 retention and N mineralization from decomposing rye that has been terminated. In a corn and soybean system in central Iowa, we investigated how cover crop presence, herbicide type, and herbicide timing affect soil nitrate, cover crop nitrogen accumulation, and cover crop decomposition. Herbicides included in the study were glyphosate and paraquat, which have different modes of action − inhibition of protein synthesis and cell lysis, respectively. Two rye termination times before soybean were tested to simulate two different farmer rye management decisions: 1) termination of all rye 10 days before corn planting but regardless of the following crop, or 2) termination of rye at two separate dates, depending on the following crop (corn or soybeans). An early termination date occurred at least 10 days before corn seeding as is recommended by Sustainable Agriculture Research and Education (Clark, 2007), and a late termination date occurred several days before soybean seeding. On average, the late termination date was 28 days after early termination. Soil nitrate-associated-nitrogen (NO3-N) was sampled weekly throughout the growing season. In 2014, rye cover crop aboveground biomass immobilized 28 and 32 kg N ha-1 with carbon:nitrogen (C:N) ratios of 11:1 and 17:1 (early and late termination, respectively). In 2015, rye cover crop aboveground biomass immobilized 28 and 89 kg N ha-1, with C:N ratios of 17:1 and 31:1 (early and late termination, respectively). For at least 2 weeks before termination and one to three weeks following termination, rye significantly reduced fall and spring soil nitrate concentrations by an average of 31% (p<0.1). Soil NO3-N and decomposing rye aboveground biomass responses to herbicide treatment was variable across years. A repeated measures analysis of variance indicates that, compared to no cover crop and early-terminated cover crop treatments, soil NO3-N concentrations in the late-terminated cover crop treatment remained an average of 71% lower around the time of late termination (p<0.1). Terminating rye as late as possible before soybean planting will maximize cover crop N retention when NO3-N loss is greatest in Iowa. Cereal rye cover crop before soybean has great potential to reduce agricultural impacts on water quality without impacting yield.