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An experiment was conducted at a depressional (lowland) and an upland site in sandy soils to evaluate the effects of surface run-off on the transport of agricultural chemicals to ground water. Approximately 16.5 cm of water was applied to both sites during the experiment, representing a natural precipitation event with a recurrence interval of approximately 100 years. Run-off was quantified at the lowland site and was not detected at the upland site during the experiment. Run-off of water to the lowland site was the most important factor affecting differences in the concentrations and fluxes of the agricultural chemicals between the two sites. Run-off of water to the lowland site appears to have played a dual role by diluting chemical concentrations in the unsaturated zone as well as increasing the concentrations at the water table, compared to the upland site. Concentrations of chloride, nitrate and atrazine plus metabolites were noticeably greater at the water table than in the unsaturated zone at both sites. The estimated mass flux of chloride and nitrate to the water table during the test were 5–2 times greater, respectively, at the lowland site compared to the upland site, whereas the flux of sulfate and atrazine plus metabolites was slightly greater at the upland site. Results indicate that matrix flow of water and chemicals was the primary process causing the observed differences between the two sites. Results of the experiment illustrate the effects of heterogeneity and the complexity of evaluating chemical transport through the unsaturated zone.