In the Chenango River Basin, New York, glacial valley-fill unconfined and confined aquifers are an important source of drinking-water supplies. The U.S. Geological Survey developed three-dimensional groundwater-flow models (MODFLOW-NWT code) of three study areas in the basin to improve understanding of groundwater flow and delineate areas contributing recharge to 16 production wells as part of an effort to protect the source of water to these wells. The modeled areas were the Cortland study area in Cortland County (CCSA), Greene study area (GSA), and the Cincinnatus study area (CSA). Production wells in CCSA tap unconfined aquifers, whereas the production wells in GSA and CSA are screened in confined aquifers. The CCSA, which has an extensive calibration dataset, was calibrated by nonlinear regression and included a prediction uncertainty analysis. The GSA and CSA were manually calibrated because of the sparse model design and calibration information. The groundwater-flow models along with particle tracking (MODPATH code) were used to simulate water levels, base flows, water budgets, and flow paths. The USGS data release contains all the input and output files and source codes for the simulations described in the associated report: https//doi.org/10.3133/sir20215083.