The flood-controlled Okavango Delta in Botswana is an endoreic alluvial fan system developing within the arid to semi- arid Kalahari Desert. The Delta sustains a unique association of ecosystems, from rivers to floodplains, riverine forests to savanna forests. This complex environment is nearly pristine from anthropic activity but its preservation, especially in the face of global change, requires a detailed understanding of the functioning and evolution of its ecosystems. In this work we describe extensive tree dieback in the savanna forest of southern Chiefs Island, the largest permanently emerged island of the Delta. While tree dieback is generally linked to drought, extreme temperatures, fire or increased biotic attacks, we suggest that the destruction in the years 2009–2012 of the Acacia sp. and Colophospernum mopane dominated forest unexpectedly results from drowning through soil water logging associated to a series of successive exceptional floods and abundant rainfall seasons. This result highlights the necessity of transdisciplinary studies in understanding the autogenic functioning of the Delta as a prerequisite to describe the effects of global change.