The Okavango Delta is renowned as an extraordinary ecosystem of high biodiversity, listed as both a Ramsar and World Heritage Site, with part protected in the Moremi Game Reserve. This extensive floodplain ecosystem has 444 recorded bird species, with just under a quarter of these waterbirds, including at least 16 breeding and 4 threatened (1 endangered, 3 vulnerable) species. Despite the global importance of this ecosystem, and its transboundary nature, there are surprisingly few long-term assessments of status of the ecosystem or waterbird communities, a key indicator of ecosystem health, with threats such as upstream water extraction, and climate change threatening its outstanding biodiversity. We compiled a comprehensive 53-year dataset comprised of citizen science and other datasets (1970–2019), on 36 waterbird species (Anhingidae, Ardeidae, Ciconiidae, Gruidae, Pelecanidae, Phalacrocoracidae, and Phoenicopteridae), including eight waterbird breeding colonies in the Okavango Delta. We investigated trends in waterbird biodiversity as well as responses to temperature, flow, flooding, and local rainfall. Waterbird breeding colonies were associated with relatively high areas of riparian woodland, and experienced moderate flooding frequencies (> 1 in 5 years). Total abundance of all 36 waterbird species was positively related to river flows. Despite increased citizen science effort over time, total abundance within the Okavango Delta significantly declined with declining average inundation. Four species led these declines (African darter Anhinga rufa, green-backed heron Butorides striata, slaty egret Egretta vinaceigula, squacco heron Ardeola ralloides) and one marabou stork Leptoptilos crumenifer, increasing (only sufficient data to analyse 15 species individually). Decreased inundation within the Delta and other internal factors (urbanisation, tourism, vegetation change) as well as external factors (habitat loss elsewhere) are likely driving these declines. Rigorous monitoring of waterbirds, including the eight breeding colonies across the Delta, is needed to explore these changes closely, providing baselines in the case of water resource developments on the rivers supplying the Okavango Delta. Long-term conservation of the magnificent Okavango Delta and its dependent biodiversity, including its waterbirds, is highly reliant on protection of river flows in three countries to ensure natural flooding regimes, alongside the conservation of neighbouring wetlands. Keywords: Africa, Botswana, Citizen science, Conservation.