The U.S. Geological Survey, in cooperation with the National Park Service (NPS), developed a three-dimensional groundwater-flow model to simulate climate-change-related changes in depth to the water table and depth to freshwater/saltwater interfaces for the Fire Island National Seashore, New York. An existing SEAWAT three-dimensional variable-density groundwater flow and transport model (https://doi.org/10.3133/sir20095259) was converted to a MODFLOW–NWT three-dimensional finite-difference groundwater model with the Seawater Intrusion (SWI2) package and recalibrated using the UCODE_2005 automatic calibration software. A management goal for the Fire Island National Seashore is to increase the resiliency and capacity of coastal habitat and infrastructure to withstand storms and reduce the amount of damage caused by major storms. To facilitate management of ecohydrological effects and to increase understanding of the relation between sea-level rise and groundwater, as it relates to the ecology of the maritime forests and other vegetated areas on the island, the NPS requires hydrologic information. Accelerated sea-level rise, storms, rising temperatures, and changes in patterns of precipitation are all expected to drive considerable ecological changes. This model was used to evaluate three sea-level rise scenarios with 0.2-, 0.4-, and 0.6-meter increases above the 2015 level, applied to the existing topography. An additional high-recharge scenario, with the 0.6-meter increase, was created by increasing 2015 recharge rates by 10 percent. Understanding the possible effects of sea-level rise and changes in recharge on groundwater resources will allow the NPS to allocate scarce resources to best prepare for and manage climate-change-driven changes in the groundwater system and the subsequent effects on seashore ecosystems. 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/sir20205117).