The transport and fate of agricultural chemicals in a variety of environmental settings is being evaluated as part of the U.S. Geological Survey (USGS) National Water-Quality Assessment Program. One of the locations being evaluated is a 2,700-km2 (square kilometer) regional study area in the northeastern San Joaquin Valley surrounding the city of Modesto, an area dominated by irrigated agriculture in a semi-arid climate. Ground water is a key source of water for irrigation and public supply, and exploitation of this resource has altered the natural flow system. The aquifer system is predominantly alluvial, and an unconfined to semiconfined aquifer overlies a confined aquifer in the southwestern part of the study area; these aquifers are separated by the lacustrine Corcoran Clay. A regional-scale 16-layer steady-state model of ground-water flow in the aquifer system in the regional study area was developed to provide boundary conditions for an embedded 110-layer steady-state local-scale model of part of the aquifer system overlying the Corcoran Clay along the Merced River. The purpose of the local-scale model was to develop a better understanding of the aquifer system and to provide a basis for simulation of reactive transport of agricultural chemicals. The heterogeneity of aquifer materials was explicitly incorporated into the regional and local models using information from geologic and drillers? logs of boreholes. Aquifer materials were differentiated in the regional model by the percentage of coarse-grained sediments in a cell, and in the local model by four hydrofacies (sand, silty sand, silt, and clay). The calibrated horizontal hydraulic conductivity values of the coarse-grained materials in the zone above the Corcoran Clay in the regional model and of the sand hydrofacies used in the local model were about equal (30?80 m/d [meter per day]), and the vertical hydraulic conductivity values in the same zone of the regional model (median of 0.012 m/d), which is dominated by the finer-grained materials, were about an order of magnitude less than that for the clay hydrofacies in the local model. Data used for calibrating both models included long-term hourly water-level measurements in 20 short-screened wells installed by the USGS in the Modesto and Merced River areas. Additional calibration data for the regional model included water-level measurements in 11 wells upslope and 17 wells downslope from these areas. The root mean square error was 2.3 m (meter) for all wells in the regional model and 0.8 m for only the USGS wells; the associated average errors were 0.9 m and 0.3 m, respectively. The root mean square error for the 12 USGS wells along a transect in the local model area was 0.08 m; the average error was 0.0 m. Particle tracking was used with the local model to estimate the concentration of an environmental tracer, sulfur hexafluoride, in 10 USGS transect wells near the Merced River that were sampled for this constituent. Measured and estimated concentrations in the mid-depth and deepest wells, which would be most sensitive to errors in hydraulic conductivity estimates, were consistent. The combined results of particle tracking and sulfur hexafluoride analysis suggest that most water sampled from the transect wells was recharged less that 25 years ago.