A three-dimensional, GSFLOW model was developed to simulate and quantify the hydrologic system of the Yucaipa subbasin. The model was calibrated to conditions from 1970 to 2014, the period for which data are most complete and reliable. The model was used to (1) quantify the effects of historical and potential water-resource development induced by climate changes and human-related activities, and (2) to derive components of the daily water budgets for the components of the integrated model for calendar years 1970–2014 (long-term average), with particular attention given to groundwater budgets for dry and wet periods. The model also was used to assess the effects of pumping and climate stresses on hydrologic-budget components in 12 groundwater subareas within the Yucaipa subbasin. This USGS data release contains all of the input and output files for the simulations described in the associated model documentation report (https://doi.org/10.3133/sir20215118). This data release also includes (1) Zonal budget code, input, and output files , (2) source code for GSFLOW, PEST++, and zone budget executable, (3) PEST++ files used in model calibration, and (4) ancillary files that might be useful for future model users.