Tile drain effluents from two adjacent agricultural systems (a mixed tree intercrop and a monocrop) were collected from April to November during 2005 and 2006. The effluents were analyzed for nitrate, ammonium and a biotracer of 'Escherichia coli' resistant to nalidixic acid (' E. coli' NAR). The biotracer was mixed with water and surface applied in April of each year. Nitrate levels were similar in 2005 (57.37 and 54.74 kg ha-1 leached from the monocrop and intercrop sites, respectively), but much higher in the monocrop effluent (164.67 kg ha-1) than that of the intercrop (88.59 kg ha-1) in 2006. Ammonium concentrations were very low over the duration of the study. Few significant differences were found in 'E. coli' NAR concentrations in the tile drain effluent; however, where there were differences, more colony forming units were found in the monocrop effluent than that of the intercrop. No differences were found in concentration of 'E. coli' NAR 'in situ ' in the effluents of the monocrop and intercrop treatments; however, the presence of tree roots had a negative impact on the biotracer levels. Overall, the intercrop system studied appeared to mitigate movement of NO 3-N and 'E. coli' NAR to the groundwater, but more research is needed to determine the mechanisms.