Accounting for all N fluxes and obtaining a complete N balance in agricultural watersheds is very challenging due to the inherent complexity of the N cycle, and the difficulty in directly measuring various fluxes. Combining the expertise of several research groups, we conducted detailed measurements of N pools and fluxes in a 9900 ha agricultural watershed (tile drained Mollisols, corn and soybean) in east-central Illinois for a two-year period, establishing a relatively complete N mass balance. Fertilizer N and N2 fixation dominated inputs, and grain export dominated outputs. Precipitation during 2001 was below average, while 2002 matched the 30 yr average for Champaign County. However, monthly rainfall was above average in May and June of 2002, which flooded fields and produced high tile and river flows. Similar to tile loads, river export was 21 and 50 kg N/ha/yr in 2001 and 2002. We estimated field denitrification to be an important flux during the wet spring of 2002 (35 kg N/ha/yr), with shallow groundwater (1 to 13 kg N/ha/yr) and in-stream denitrification (0.4 to 0.5 kg N/ha/yr) much less important either year. Overall the watershed N balance showed that soil depletion of organic N pools was occurring (about 37 kg N/ha/yr). These results quantitatively support previous watershed input/output work that indicated in these productive, tile drained soils current management practices are leading to a very slow depletion of soil organic N. Without depletion of soil organic N, there is not enough inorganic N added to the soils each year to account for current sinks. The slow depletion of soil organic N may be due to decoupled C and N biogeochemical cycles where N is lost as nitrate because it is not incorporated into more stable organic N forms and is present in high concentrations during periods of high soil leaching.