Multiproxy palaeoenvironmental analyses represent a promising tool for complex reconstructions of continent-sea or air-sea interactions in shallow marine environments. This is in particular illustrated by the case of strong climatic variations in the late Pleistocene to mid-Holocene. A unique combination of geochemical proxies (143Nd/144Nd, 87Sr/86Sr, δ18O and δ13C isotope analyses, n-alkane analysis and biomarker study) together with micropalaeontological data (foraminifera, calcareous nannoplankton and diatoms) allowed to precisely characterise two marine floodings (mid-Holocene and late Pleistocene) in the Zanzibar Channel (NW Indian Ocean, Tanzania). The climate of the late Pleistocene interval was arid compared to the Holocene. The fully oligotrophic environment characteristic of the late Pleistocene flooding (∼115–130 ka) was episodically interrupted by intervals of intense rainfall with episodes of increased nutrient input during the mid-Holocene (∼5–10 ka). The dominance of seaweed meadows in the Holocene and late Pleistocene contrasts with the modern environment dominated by seagrass ecosystems. Relatively non-radiogenic εNd signatures in the Zanzibar Channel during the Holocene and late Pleistocene indicate a strong influence of riverine input draining the Precambrian basement on the African mainland. The main inflow of seawater was from the south, consistent with the flow direction of the East African Coastal Current and the directions of the March to October monsoon winds. A promising tool for future applications as indicators of seagrass/seaweed meadow type ecosystems may be the presence of specific diatom taxa.