Coastal wetlands have a long history of degradation and destruction due to human development. Now recognized as one of the most productive ecosystems in the world, substantial efforts are being made to restore this critical habitat. While wetland restoration efforts are generally viewed as beneficial in terms of providing wildlife habitat and flood control, they are often accompanied by dramatic physical and chemical changes that may result in unintended consequences, which are rarely studied. Alviso Slough, a tidal slough in South San Francisco Bay, California, is the site of an ongoing effort to restore former salt-production ponds to intertidal marsh habitat. Restoration is complicated by the fact that (1) the ponds undergoing restoration are severely subsided and (2) subsurface sediments within the slough and surrounding ponds are contaminated with legacy mercury deposits. Due to concerns regarding mercury remobilization, restoration has proceeded in a cautious, methodical manner. To assess the amount of legacy mercury remobilized since restoration began, we developed a technique of combining high-resolution, biannual measurements of bathymetric scour with mercury concentration measurements from sediment cores. We estimate that 52 kg (±3) of mercury was remobilized in the 6 years since restoration began. Net bathymetric change analyses revealed seasonal trends of peak erosion during the winter months and little to no net change during summer months. Our analyses provide crucial insight on the spatial and temporal scales of geomorphic evolution within a tidal slough resulting from both natural (seasonal) variability and restoration actions. The technique presented here could be applied to other study sites and various sediment-associated contaminants of concern to aid in the design and management of restoration projects aiming to minimize negative impacts from legacy contaminants.