The triangle between the Kavango and Kunene rivers is drained by the Cuvelai, an ephemeral and deltaic drainage system covering more than 100 000 km2. In good rainfall years, the area becomes populated by fish communities dominated by five species migrating southward towards the endorheic Etosha Pan, the basin’s terminal sump. When water dries up, fish subsequently die-off and their sudden appearance in rainy years has captivated scientists for decades. The current study was prompted by hitherto untapped indigenous knowledge through narratives of opportunistic fish harvesting of migrating fish at temporary connections between the Kunene River and the Cuvelai- Etosha Basin. A reconnaissance fish survey in 2017 was complemented by digital satellite images and elevation data analyses. Results support the presence of at least three major ephemeral fish migration routes. The dominant fish genera migrating upstream in Kunene tributaries comprise Enteromius, Oreochromis and Clarias, all eurytopic and known to undertake upstream, lateral and downstream migrations on floodplains. Although other notable fish refugia in the Cuvelai–Etosha Basin are yet to be identified, there is a necessity for the protection and management of these migration routes in tandem with studies on the nature and extent of this inter-basin fish migration under climate change and variability. Keywords: Clarias, Enteromius, Etosha Pan, fish migration, indistinct water divide, Kunene River, Oreochromis.