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One of the largest freshwater estuarine systems on Earth, Green Bay receives freshwater runoff from its land watershed and cold-water intrusions from Lake Michigan. Southern Green Bay is a designated area of concern (AOC) due to ecosystem degradation, contaminated sediments, and poor water quality. Successful restoration of aquatic systems requires a clear understanding of their circulation and thermal regimes. Using a state-of-the-art numerical ocean model, this study examines the effect of variability in tributary inflows and the related lake intrusions on the circulation and thermal regime in Green Bay and on the mass and heat fluxes between lower- and upper–Green Bay areas. Our findings indicate that tributaries influence the circulation and thermal regime, locally and throughout the bay, and that the impact is more significant in hydrologically wet years. Model simulations showed evidence of small net transport out of lower Green Bay. This analysis of the simultaneous effects of tributary flows and lake intrusions in Green Bay can contribute to understanding the dynamics of freshwater estuaries and improve the planning of future restoration projects. [ABSTRACT FROM AUTHOR]