Invasive carp can negatively affect waterbirds through habitat degradation, including removal of submersed aquatic vegetation (SAV). At a freshwater coastal marsh of great ecological and cultural significance, we excluded invasive common carp (Cyprinus carpio) with the goal of restoring the marsh to historical conditions to support fall-migrating waterfowl. We used a multi-pronged approach to assess the response of ducks and SAV to carp exclusion by leveraging historical duck and SAV surveys and collecting new data for six years post-exclusion on density and distribution of ducks within the marsh, SAV response, and refueling performance (as indexed by plasma-lipid metabolites) by two species of diving ducks. We found that fall-migrating duck numbers and total SAV extent rebounded to historical levels (1970s). There was a 339% increase in diving duck density and a nearly 400% increase in dabbling duck density between the pre- (i.e., 2000s) and post-exclusion periods. Diving ducks were more likely to be observed associated with SAV within the marsh, whereas dabbling ducks responded to emergent vegetation extent and water levels. Refueling performance was stable post-exclusion, despite increased numbers of ducks using the marsh, indicating that marsh habitat quality was sufficient. Some aspects of the marsh recovery remain in question, including possible shifts in SAV community composition. Overall, the carp exclusion has successfully improved the quality of habitat for migrating ducks.