Long term changes in catches of two sardinella species off equatorial West Africa seem inconsistent with their thermal preferences. Sardinella maderensis is usually fished during the warm season in low salinity waters, while S. aurita is associated with cold upwelled waters. However, in the Congo fisheries, S. maderensis dominated the catches from 1964 to 1983, when temperatures were moderate or cool; subsequently S. aurita became the most important from 1984 onward, as there was pronounced warming. The movement of water masses related to Atlantic Niño-like episodes explains this paradox. These warm events are associated with enhancement of the equatorial counter currents. When the eastward transport strengthens south of the equator (Benguela Niño), it drives an influx of warm water towards Angola, which repels Sardinella aurita northwards. Then, trapped near the coast by the subsuperficial warm water intrusion and the deviation of the Congo River plume, S. aurita becomes more concentrated and vulnerable to fishing. This is the most frequent situation during warm events. However, when the anomaly involves the north equatorial counter current (Guinea Niño), we assume that this surge of water in the Bight of Biafra leads to a water leakage toward the south, along the Gabon coast. This warm and low salinity water tongue, homologous to the Peruvian El Niño current, would drive Sardinella maderensis towards the Congo fisheries, but would force Sardinella aurita offshore making it less accessible to the fisheries. This situation is likely to have occurred in 1987–1988 when there were large catches of several species linked to brackish waters (bongas, Pseudotolithus, soles, catfish, sharks and spiny lobsters). On the contrary, decadal variations of catches of the two species are consistent with regime shifts of the Congo River: Sardinella maderensis is dominant when the outflow is above average (1960s and 1970s) and is replaced by Sardinella aurita when the runoff is weak (1980s and 1990s). In Angola, the catches of horse mackerel shift southwards during the warm years preceding 1976, then northwards during a cool period ending in 1983. From 1984, the abundance of horse mackerels over the shelf increases after warm events.