Streamgaging weirs, like the ones used by the U.S. Geological Survey (USGS), play a critical role in providing accurate and stable streamflow data, but their presence can affect the passage of diadromous fish species such as river herring and American shad. In some situations, weirs existing in rivers and streams are no longer used because they were part of a farm irrigation system or some type of industrial operation. Removal of those structures can restore the river to a more natural state in those reaches. The weir at the USGS streamgage 01402000 Millstone River at Blackwells Mills, New Jersey is not an obsolete relic from an old agricultural or industrial operation rather it was purposefully built as a hydraulic control structure that provides precise and stable control for the measurement of stage and computation of continuous streamflow. To satisfy the dual need of maintaining accurate streamflow data and improved fish passage for select species of fish during migration season, the USGS proposed development and evaluation of two alternative weir designs that would meet the criteria established for successful passage of the American shad, alewife, and blueback herring during their migration season from April 14 through May 28 of each year. The designs also are needed to maintain adequate control of the upstream pool elevation necessary for precise computation of streamflow that is used by state agencies for municipal water-supply purposes for surrounding communities. Alternative weir designs incorporating two different weir modifications within the center section of the Blackwells Mills weir were modeled using two-dimensional hydraulic modeling software (HEC-RAS) and three-dimensional computational fluid dynamics software (FLOW 3D HYDRO) to simultaneously evaluate conditions for passage of the target fish species and impacts to streamflow computation at the Blackwells Mills streamgage. The models were calibrated to existing conditions around the weir location using surveyed elevation data and recorded stage, streamflow, and velocity in the Millstone River. This data release contains the input and output data for the two models used to complete the analysis of the alternative weir designs. The contents of this data release support the following publication: Suro, T.P., Niemoczynski, M.J., Mulligan, K.M., 2026, Analysis of alternative weir designs for improved passage of select fish at the U.S. Geological Survey streamgaging weir at Blackwells Mills, New Jersey: U.S. Geological Survey Scientific Investigations Report 2026-5002, https://doi.org/10.3133/sir20265002.