The operation and economic profitability of modern energy systems is constrained by the availability of renewable energy and water resources. Lower water availability due to climate change, higher demand and increased water consumption for non-energy and energy needs may cause problems in Africa. In most African power systems, hydropower is a dominant renewable energy resource, and interconnection capacities are usually limited or unreliable. This paper describes a new modelling framework for analysing the water-energy nexus in the African Power Pools. This framework includes soft linking between two models: the LISFLOOD model is used to generate hydrological inputs and the Dispa-SET model is used for mid-term hydrothermal coordination and optimal unit commitment and power dispatch over the whole African continent. The results show a good agreement between the model outputs and the historical values, despite data-related limitations. Furthermore, the simulations provide hourly time series of electricity generation at the plant level in a robust way. It appears that some African power pools heavily rely on the availability of freshwater resources, while others are less dependent. In the long term, the dependence of the power system on water resources is likely to increase to meet the increasing electricity demand in Africa. •Robust and highly detailed analysis of water-energy nexus in African power pools.•Open source soft-linking framework between LISFLOOD and Dispa-SET models.•First open-source unit commitment and power dispatch model of African power pools.•A compilation of diverse data sources used for the integrated water-energy modelling.•Examination of current and future electricity situation and potential of power trade.