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Despite improvements in the use of soil conservation practices, crop rotation and managed fertilizer applications, large losses of nitrogen (N) in runoff continue to occur from row-cropped watersheds. Increasing requirements for implementing water quality standards in the United States, has increased pressure for the development of research-based guidelines to reduce N losses from agricultural runoff. The objectives of this study were to examine the effects of management, watershed characteristics, and precipitation on TN and nitrate-N (NO3--N) loss over time by comparing losses on three adjacent watersheds with claypan soils. The three adjacent north-facing, corn-soybean rotational watersheds in northeastern Missouri were instrumented with H-flumes, water samplers, and flow-monitoring devices in 1991. Runoff samples from each individual rainfall event between 1991 and 1997 were analyzed for TN and NO3--N concentrations. The 7-year mean annual TN losses on the three watersheds ranged from 13 to 19 kg ha-1 with a mean of 16 kg ha-1. Nitrate-N losses ranged from 8 to 14 kg ha-1 with a mean of 11 kg ha-1. During the study, 67% of the TN was lost as NO3--N with a range from 22% in 1997 to 76% in 1996. The mean annual TN losses for corn and soybean years during the study were 30.7 and 5.7 kg ha-1, respectively. Significantly higher loss (57%) of N from watersheds occurred during the period between fall harvest and spring planting when crops were not present (referred to as the “fallow” period in this paper; 86.8 kg ha-1) compared to N losses during the cropping period (64.5 kg ha-1). In 1994, 96% of the annual TN loss and 98% of the annual NO3--N loss occurred during the fallow period. In contrast, the lowest fallow period losses of TN (19%) and NO3--N (14%) occurred in 1993. The watershed-mean TN and NO3--N losses in 1993 alone accounted for 44 and 46% of the total losses observed over the 7-year period because during that year the study area received 142% of the normal precipitation. When the study area received 51% of the annual precipitation before planting in 1996, the TN and NO3--N losses accounted for 34 and 38% of the 7-year loss, respectively. Nitrogen fertilizer that was applied in 1993 and 1996 may also have contributed to the observed large losses. The results of this study suggest that the maintenance of a suitable vegetative cover throughout the year could reduce runoff and lower TN and NO3--N loss from agricultural watersheds under a corn-soybean rotation.