The Okavango Delta, Botswana, is a major wetland surrounded by the Kalahari Desert. The delta supports a diverse fish fauna that depends on highly seasonal flooding from inflowing rivers, and on the actions of ecosystem engineers (hippopotamuses, elephants, and termites), for creation and maintenance of their habitats. Conflicts in resource use, especially water, are likely to affect fish populations and the Okavango ecosystem in the near future. We present conceptual models of this remarkable aquatic ecosystem in relation to fish and fisheries as the basis for future research and conservation efforts. Developing understanding of the environmental flow requirements of the delta is key to the management of the Okavango Delta as an ecosystem supporting diverse and abundant fish and wildlife. Once developed, this understanding can be used to allocate water within the Okavango watershed.