Multilevel, double-packer slug tests were performed in open core holes to characterize heterogeneity within a flat-lying, fractured carbonate aquifer. Hydraulic conductivity was measured to vary by approximately three orders of magnitude in the vertical direction and by as much as two orders of magnitude in the horizontal direction. In general, hydraulic conductivity decreased with distance from the bedrock free-surface, as the degree of fracturing decreased. The results of the multilevel slug tests provided the basis for hydraulic conductivity zonation within a two-dimensional finite-element model, which simulated nitrate transport in cross section. In simulation of steady-state flow, several shallow, local ground-water flow systems occurred with exit points that are consistent with springs observable in the field. Yearly rotating crops of corn and soybeans were simulated with nitrate source concentrations based on pore water measurements in the lower soil zones of the field site. The majority of simulated nitrate movement occurred within shallow, localized ground-water flow systems, where much of the nitrate exited the system relatively soon after entering, without appreciable accumulation of nitrate through the years. Based on these results, a monitoring program with a relatively high spatial and temporal resolution in the shallow, localized ground-water flow systems was required in order to characterize nitrate concentrations in the ground water. Regional water quality surveys that involve a random sampling of existing, widely spaced wells would likely miss detecting the locations and times of high nitrate concentrations in ground water.