Unguja Ukuu, located on the Zanzibar Archipelago, eastern Africa, was an active Indian Ocean trading settlement from the mid-first millennium until the early second millennium AD. As part of recent archaeological excavations aimed at understanding the site’s transregional trade networks, geoarchaeological analyses were undertaken to document the geomorphic context of the ancient settlement. Here, we outline the results of these field and laboratory studies to discuss patterns of anthropogenic sediment deposition. Unguja Ukuu’s deep coastal stratigraphy appears to record progradation of an inhabited back-reef shore from the mid-seventh to the nineth centuries AD, perhaps in the wake of an earlier middle to late Holocene marine transgression. Excavations on the back-beach show that deposits associated with the ancient settlement include interlayered middens, paleofloors, and backshore sands and, in later phases, a peri-urban dump with dark-earth-type anthrosols developed on these deposits. Coastal progradation appears to have been driven in part by the accumulation of anthropogenic detritus and compaction of ancient surfaces. We hypothesize how the inherited, submerged relic Late Pleistocene geomorphology of the intertidal zone and later Holocene sediment supply from the hinterland may have supported the emergence of Unguja Ukuu as a trading locale, and possibly contributed to its decline in the early second millennium AD.