This paper documents the first Holocene palaeoecological record for the Okavango Delta, northwest Botswana. Sedimentological, stable carbon isotope and palynological data, supported by conventional and AMS radiocarbon assays, are presented from coring sites at Gauxa Lagoon and the Ncamasere and Tamacha valleys along the western margin of the Okavango Panhandle. Earliest Holocene vegetation patterns are not readily distinguished at the three sites, owing to poor pollen preservation conditions. A wet phase or period of enhanced Okavango flooding is tentatively identified around 9000 BP on the basis of increased accumulation of organic matter within floodplain sediments. Palynological and sedimentological data, combined with stable carbon isotope analyses, suggest that relatively dry conditions extended from 7000 to 4000 BP (punctuated by a wet phase at around 6000 BP). This is interpreted as indicating reduced rainfall over the Okavango headwaters in Angola. Conditions from around 4000 BP became progressively wetter, initially in response to increased water throughputs via the Okavango system. Wettest conditions occurred from 2300 to 1000 BP due to a combination of increased regional rainfall and raised Okavango flood levels. Conditions approach those of the present day after this time. A major shift from grass- to sedge-dominated vegetation communities, apparent at all three sites in the past thousand years, is attributed to anthropogenic disturbance. These changes are subsequently discussed in light of regional continental and marine palaeoenvironmental records, and the implications for the future management of the Okavango River considered.