Applying a coastal-geoarchaeological approach, we synthesize stratigraphic, sedimentological, mollusk-zooarchaeological, and radiometric datasets from recent excavations and sediment coring at Harbor Key (8MA15)—a shell-terraformed Native mound complex within Tampa Bay, on the central peninsular Gulf Coast of Florida. We significantly revise the chronological understanding of the site and place it among the relatively few early civic-ceremonial centers in the region. Analyses of submound contexts revealed that the early first millennium mound center was constructed atop a platform of sand and ex situ cultural shell deposits that were reworked during ancient storm landfalls around 2000 BP. We situate Harbor Key within a seascape-scale stratigraphic and paleoenvironmental framework and show that the shellworks comprise an artificial barrier protecting the leeward estuary basin (and productive inshore wetlands) from high-energy conditions of the open bay and swells from the Gulf of Mexico. The sedimentary and archaeological records attest to the long-term history of morphodynamic interaction between coastal processes and Indigenous shell terraforming in the region and suggest that early first millennium mound building in Tampa Bay was tied to the recognition and reuse of antecedent shellworks and the persistent management of encompassing cultural seascapes.