A calibrated groundwater flow model for a contaminated site can provide substantial information for assessing and improving hydraulic measures implemented for remediation. We developed a three-dimensional transient groundwater flow model for a contaminated mountainous site at which interim corrective measures were initiated to limit further spreading of contaminants. This flow model accounts for complex geologic units that vary considerably in thickness, slope, and hydrogeologic properties, as well as large seasonal fluctuations of the groundwater table and flow rates. Other significant factors are local recharge from leaking underground storm drains and recharge from steep uphill areas. The zonation method was employed to account for the clustering of high and low hydraulic conductivities measured in a geologic unit. A composite model was used to represent the bulk effect of thin layers of relatively high hydraulic conductivity found within bedrock of otherwise low conductivity. The inverse simulator iTOUGH2 was used to calibrate the model for the distribution of rock properties. The model was initially calibrated using data collected between 1994 and 1996. To check the validity of the model, it was subsequently applied to predicting groundwater level fluctuation and groundwater flux between 1996 and 1998. Comparison of simulated and measured data demonstrated that the model is capable of predicting the complex flow reasonably well. Advective transport was approximated using pathways of particles originating from source areas of the plumes. The advective transport approximation was in good agreement with the trend of contaminant plumes observed during the same years. The validated model was then refined to focus on a subsection of the large system. The refined model showed that most of the hydraulic measures implemented for remediation are effective.