This study aims to resolve a potential water conflict between the upper catchment communities of the Okavango River Basin and the downward communities in the Okavango Delta. A model to payment for ecosystem services is developed at the basin level, recognizing spatial diversity and water flows. It addresses four objectives: (1) To assess relationships between water consumption and land use from a spatial perspective. (2) To estimate water availability under current land use as a reference without any water policy intervention. (3) To optimize water flow generation as intended for getting ecosystem services. This is based on the mechanism of payments for ecosystem services, specifically in terms of land use change as stewardship. (4) To compensate farmers for economic losses due to upstream land use changes. Our study suggests that an integrated basin management should consider payments for ecosystem services to incentivize forest conservation. The annual payments of US$28.7 million could encourage farmers upstream to change their land uses from deforestation to forest conservation. With compensation, approximately 8.7 million hectares of Miombo forests would be maintained in the basin, which would secure 3656 million m3 of water during the rainy season and subsequently benefit the Delta in the dry season.