This article addresses two related themes: the response of coastal communities to the impact of environmental processes and human actions as reflected in archaeology, and threats to the archaeological record emanating from current natural and human agencies. The geographical context is the entire east coast of Africa, although emphasis is placed on Swahili settlements in the light of their long-standing dependence upon maritime resources and trading opportunities. Evidence is derived from documentary sources and field studies with detailed data from Kilwa, Tanzania. Physical conditions are relatively benign, but threats are identified in adverse weather events, erosion, and sedimentation processes. Knowledge of past climatic impacts upon shipping is restricted by limited research of the off-shore environment. On-shore, the archaeological record provides evidence of protective construction work, possibly where erosion precipitated by removal of mangroves. However, unless significant port investments required safeguarding, relocation of landing area and settlement was principal response to erosion and sedimentation. Current threats to archaeology are far more significant both from natural processes of marine erosion and vegetation growth encouraged by urban decline and neglect. Limited legislation and resources are seen as the greatest impediments to investigation and protection of heritage from urban and tourism inspired development in future.