The U.S. Geological Survey (USGS), in cooperation with the U.S. Army Corps of Engineers Engineer Research and Development Center and the U.S. Environmental Protection Agency, developed a predictive, mechanistic, three-dimensional hydrodynamic model for the St. Louis River Estuary (SLRE), Minnesota. This model was developed with Environmental Fluid Dynamics Code (EFDC), a grid-based, surface-water modeling package for simulating three-dimensional circulation, mass transport, sediments, and biogeochemical processes. The new model predicts discharge, water-surface elevations, flow velocity, and water temperature. The model was calibrated using data collected from April 2016 through November 2016 and validated with data collected from April 2017 through November 2017. The report summarizes both the development and calibration of the new model.