Alpha diversity in the Okavango Delta is an order of magnitude higher than any other eco-region in southern Africa, except for the Cape Fynbos. How is this diversity related to habitat and landscape diversity? Here, we demonstrate that all three scales of diversity are driven by pulsing phenomena across hierarchical temporal and spatial scales. Hydro-climate in the Okavango River Basin is highly variable: seasonal rainfall produces a pronounced pulse each year, superimposed on a multi-decadal wet-dry cyclicity, against a backdrop of flow-sediment-vegetation feedbacks in the Delta apex, which produce an episodic channel avulsion process at the centennial scale. Each of these pulses maintains diversity at corresponding scales in the Delta.