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The Little Vermilion River (LVR) watershed in east central Illinois is an example of a watershed with altered hydrology from subsurface drainage systems. A continuous monitoring study has been conducted from 1991 to 2004 on this watershed to evaluate the effects of agricultural management practices on fertilizer and pesticide transport in subsurface flow. Water quality results obtained from four of the seven subsurface drainage stations in the LVR watershed for the period 1991-2000 are presented in this paper. The long-term monitoring results indicated that the nitrate-N concentration in subsurface drains varied depending on fertilizer application timing, rates and methods. Elevated nitrate concentrations were observed in the first few months of growing seasons. Long-term average annual flow weighted nitrate- N concentrations were lower than 10 mg/L under no-till system. Sites with reduced tillage practices had 10-year average annual flow weighted nitrate-N concentrations higher than MCL. Atrazine concentrations were lower than 3 g/L in most water samples. Nevertheless, atrazine concentrations exceeded MCL in several incidents for all sites during the study period. Major atrazine loss in drainage water occurred within three months of atrazine application.