A three-dimensional groundwater flow model was developed in 1997 to evaluate the groundwater flow system at Puget Sound Naval Shipyard, Naval Base Kitsap, Bremerton, Washington (https://pubs.er.usgs.gov/publication/wri964147). In 2016, a regional groundwater flow model for the greater Kitsap Peninsula was developed (https://pubs.er.usgs.gov/publication/sir20165052). Using information from the 2016 regional model, the 1997 groundwater flow model for the Puget Sound Naval Shipyard was updated with a new interpretation of the underlying hydrogeologic units, a refined model grid, and improved recharge estimates. A steady-state model version was constructed in MODFLOW-NWT to simulate equilibrium conditions. MODPATH forward and backward particle tracking simulations were then run using output from the steady-state MODFLOW-NWT model. This data release contains the input and output files for the simulations described in the associated model documentation report (https://doi.org/10.3133/ofr20161135).