Under the impact of natural and anthropogenic climate variability, upwelling systems are known to change their properties leading to associated regime shifts in marine ecosystems. These often impact commercial fisheries and societies dependent on them. In a region where in situ hydrographic and biological marine data are scarce, this study uses a combination of remote sensing and ocean modelling to show how a stable seasonal upwelling off the Kenyan coast shifted into the territorial waters of neighboring Tanzania under the influence of the unique 1997/98 El Niño and positive Indian Ocean Dipole event. The formation of an anticyclonic gyre adjacent to the Kenyan/Tanzanian coast led to a reorganization of the surface currents and caused the southward migration of the Somali–Zanzibar confluence zone and is attributed to anomalous wind stress curl over the central Indian Ocean. This caused the lowest observed chlorophyll-a over the North Kenya banks (Kenya), while it reached its historical maximum off Dar Es Salaam (Tanzanian waters). We demonstrate that this situation is specific to the 1997/98 El Niño when compared with other the super El-Niño events of 1972,73, 1982–83 and 2015–16. Despite the lack of available fishery data in the region, the local ecosystem changes that the shift of this upwelling may have caused are discussed based on the literature. The likely negative impacts on local fish stocks in Kenya, affecting fishers’ livelihoods and food security, and the temporary increase in pelagic fishery species’ productivity in Tanzania are highlighted. Finally, we discuss how satellite observations may assist fisheries management bodies to anticipate low productivity periods, and mitigate their potentially negative economic impacts.