A high-resolution multiproxy sedimentary record comprising pollen, charcoal, trace element, stratigraphy and particle size data is used to reveal environmental changes from the mangrove ecosystem at Unguja Ukuu, Zanzibar, Tanzania, over the last 5000 years. Historical human–environment interactions over the last millennia are explored by a comparison of the stratigraphic and archaeological data. The area was characterised by a mixture of mangrove forest and beaches, indicating a low level of tidal inundation to at least 3300 BCE. From 2750 BCE, mangrove forest expanded as the area experienced sea-level rise. Further sea-level rise is recorded between 600 and 1100 CE, indicated by the pollen record, particle size analysis and the presence of shell fragments. After 1100 CE, mangrove forest decreased with back mangrove species increasing, indicating a falling sea level. Cocos nucifera decreased after 1900 CE, which reflects a recent sea-level rise and possibly a phase of exploitation. Cereal pollen shows a high presence at around 1500 CE, which coincided with the arrival of the Portuguese on Zanzibar and the transition to Omani colonisation. The sedimentation rate in the core top indicates that mangroves in Unguja Ukuu cannot keep pace with the current rate of sea-level rise.