Climate change and climate variability impacts such as rising sea levels have the potential to exacerbate seawater intrusion and the strain on coastal freshwater resources in already stressed groundwater basins such as those in the Pajaro Valley groundwater basin, California. The U.S. Geological Survey (USGS) developed the Pajaro Valley Hydrologic model (PVHM) to quantitatively assess aquifer-system responses to climatic variation, surface-water deliveries, and seawater intrusion.The PVHM historical model (1963-2018) was updated, extended, and re-calibrated using a combination of manual adjustments to parameters and an assisted parameter estimation PEST++ software (White et al., 2020) to minimize differences between simulated values and historical observations of streamflow, groundwater levels, and agricultural pumping. Three future climate scenarios (2013-2100) were developed for the PVHM, using three climate projections from global general circulation models (GCMs) representing hot and dry conditions, average conditions, and cool and wet conditions. The climate ensemble was used to conduct a first-order second moment uncertainty analysis of groundwater level and seawater intrusion forecasts using PEST++ software (White et al., 2020). Understanding the reliability and uncertainty of forecasts is important for developing climate adaptation strategies such as developing protective thresholds, particularly at the basin scale where the impacts are felt, and adaptation is implemented. This USGS data release contains all of the input and output files for the historical updated PVHM and the three future climate scenarios described in the associated journal article.