A three-dimensional MODFLOW-NWT model was constructed to better understand the effects of drought stress on the Cedar River alluvial aquifer, the principal source of municipal water for the City of Cedar Rapids, Iowa. Historically, the aquifer supported the production needs of the City of Cedar Rapids and surrounding area but between July 2011 and February 2013, Iowa experienced severe drought conditions that affected water availability for communities that relied on alluvial aquifers for their production needs. During that time, the City of Cedar Rapids observed water level declines in their horizontal collector wells (HCW) of as much as about 11 meters. Pumping from affected production wells had to be halted to prevent damage to the pumps and wells and caused concern about the reliability of the alluvial aquifer under future drought conditions. In 2013, the U.S. Geological Survey (USGS), in cooperation with the City of Cedar Rapids, began a study to better understand the effects of drought stress on the Cedar River alluvial aquifer using a numerical groundwater flow model which combined published hydrogeologic data with airborne, waterborne, down-hole, and land-based geophysical survey data collected from 2015 to 2017. The model (1) provided a detailed three-dimensional lithologic model of the Cedar River alluvial aquifer and surrounding area, (2) improved the conceptual model for the groundwater flow system, and (3) evaluated hydrogeologic characteristics of aquifer materials. Two models were constructed for this study. A steady-state model of mean hydrologic conditions for November 2015 and a transient model to simulate conditions from October 1, 2016, to August 31, 2018 (calibration period), and from October 1, 2011, to April 30, 2013 (simulation period). Additional scenarios using the transient model simulate drought conditions from October 2011 to April 2013 and evaluate the transient drought conditions with modifications to the riverbed. The numerical models were developed as a tool for use by water managers to better understand the potential effects of drought and increased demand on production wells. This USGS data release contains all the input and output files for the simulations described in the associated model documentation report (https://doi.org/10.3133/sir20215065).