A three-dimensional groundwater flow model of the Central Valley in California was developed to aid water managers in understanding how water moves through the aquifer system, to predict water-supply scenarios, and to address issues related to subsidence. The USGS California Water Science Center made a detailed assessment of groundwater availability of the Central Valley aquifer system, which includes: (1) the status of groundwater resources; (2) how these resources have changed over time, particularly related to subsidence; and (3) tools to assess system responses to stresses from future human uses and climate variability and change. This effort builds on previous investigations, such as the USGS Central Valley Regional Aquifer System and Analysis (CV-RASA) project and Groundwater Resources Program and several other groundwater studies in the Valley completed by Federal, State and local agencies at differing scales. The principal product of this new assessment is a tool referred to as the Central Valley Hydrologic Model version 2 (CVHM2) that accounts for integrated, variable water supply and demand, and simulates surface-water and groundwater-flow and subsidence across the entire Central Valley system. The current model was extended to incorporate a slightly larger geographic area, includes more water level and subsidence observations, uses a more-detailed depiction of subsurface geology, includes managed aquifer recharge and flux from small watersheds, and utilizes a more detailed simulation of subsidence processes. In addition, the model utilizes a specialized version of MODFLOW called the MODFLOW-One-Water Hydrologic Flow Model (MODFLOW-OWHM) to simulate groundwater and surface-water flow, irrigated agriculture, land subsidence, and other key processes in the Central Valley monthly for April 1961 through September 2019. This USGS data release contains all of the input and output files for the simulation and calibration of the CVHM2 described in the associated model documentation report (https://doi.org/10.3390/w16081189).