A three-dimensional groundwater flow model using MODFLOW-NWT was developed to evaluate historical and potential stream capture in the lower Humboldt River Basin, Nevada. The Humboldt River Basin is the only river basin that is contained entirely within the state of Nevada. The effect of groundwater pumping on the Humboldt River is not well understood. Tools are needed to determine stream capture and manage groundwater pumping in the Humboldt River Basin. Previous work has demonstrated that the river’s surface-water resource is sensitive to groundwater withdrawals, which have steadily increased since the 1950s for agriculture, municipal, and mining uses. A numerical groundwater flow model was developed for the purpose of estimating stream capture from pre-2016 and future pumping as well as for any location of potential future pumping within the lower Humboldt River Basin. The model was calibrated with historical data from 1960 through 2016. The calibrated historic model was used to evaluate historic capture and a transient predictive model was used to evaluate potential capture anywhere within the lower Humboldt River Basin, Nevada. 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/sir20235110).