A previously developed three-dimensional groundwater flow model (https://doi.org/10.3133/sir20125183) of the three primary aquifers in the region north of Aberdeen, South Dakota, was revised to assist the City of Aberdeen with water-resource planning. The principal aquifers are the Elm, Middle James, and Deep James. The numerical model is intended to be used to (1) simulate hydrologic scenarios of interest to groundwater managers and to advance the understanding of groundwater budgets and components including recharge, discharge, and aquifer storage, (2) compute historical and projected system response to natural and anthropogenic stresses, and (3) evaluate potential withdrawal scenarios to assist with water-management decisions. The three-dimensional groundwater-flow model was developed using the USGS's numerical modeling software, MODFLOW-NWT. The model included both steady-state (mean) and transient (temporally varying) conditions. Steady-state data were from October 1, 1974 to September 30, 2009, and the transient time period included data from October 1, 1974 to September 30, 2015. The model was calibrated by attempting to match simulated and measured or estimated hydraulic heads, differences in hydraulic heads between aquifers, and stream base flow. Water budgets for the model's layers area were produced with ZONEBUDGET. This USGS data release contains all of the input and output files for the model described in the associated model documentation report (http://doi.org/10.3133/sir20185137). The data release also includes (1) MODFLOW-NWT (version 1.1.4) source code, and (2) ZONEBUDGET (3.01) source code.