The abundance of two main pelagic fish species in Lake Tanganyika (Stolothrissa tanganicae and Lates stappersii) has always been observed to fluctuate considerably at different time scales. The inverse correlation between the abundance of these species has often been interpreted as the consequence of predator-prey relations (avoidance behaviour by the prey). However, currently the two species often appear spatially segregated in the lake, S. tanganicae dominating in the north while L. stappersii is generally abundant in the south where it feeds mostly on shrimps. A fluctuating abundance of the species is nevertheless observed. As these fish species have a major importance for the fisheries, we investigated the limnological variability in relation to the short-term variability of fish catches. The abundance of S. tanganicae was positively correlated to plankton biomass (r = 0.65), while water transparency (r = 0.56), depth of mixed layer (r = -0.70) and oxygenated water appeared important drivers for the abundance of L. stappersii. Alternating "mixing" and "stable" states of the epilimnion related to seasonal and internal waves variability are probably determinant for the short-term variability in abundance of S. tanganicae and L. stappersii. In the framework of this study, remote sensing has shown a potentially interesting application for fisheries research at Lake Tanganyika. We observed a close correspondence between phytoplankton blooms at the time of trade winds changes and increased catches of S. tanganicae in the south. The anti-correlated abundance of S. tanganicae and L. stappersii probably mainly reflects the underlying fluctuating limnological environment. Fisheries studies need to integrate limnological and planktonic monitoring to better understand large and complex ecosystems such as Lake Tanganyika.