Lake Tanganyika's pelagic fish sustain the second largest inland fishery in Africa and are under pressure from heavy fishing and global warming related increases in stratification. Only little is known about whether basin-scale hydrodynamics - including a more stratified north and an upwelling-driven south - lead to regional fish populations with varying ecological adaptations. Here, we examine whether the basin-scale dynamics leave distinct isotopic imprints in the pelagic fish of Lake Tanganyika, which may reveal differences in habitat, diet, or lipid content. We conducted two lake-wide campaigns during different seasons and collected physical, nutrient, chlorophyll, phytoplankton and zooplankton data. Additionally, we analyzed the pelagic fish - the clupeids Stolothrissa tanganicae, Limnothrissa miodon and four Lates species - for their isotopic and elemental carbon (C) and nitrogen (N) compositions. The δ13C values were significantly higher in the productive south after the upwelling/mixing period across all trophic levels, implying that the fish have regional foraging grounds, and thus record these latitudinal isotope gradients. However, the degree of regional isolation is insufficient to suppress lake-wide gene flow, suggesting that the fish form regional populations only on a basin-wide and seasonal scale. Based on δ15N and C:N ratios, we found no strong evidence for varying diets or lipid contents between those populations. Additional analyses revealed that isotopic variations between specimens from the same location are not linked to genetic differences. Our findings provide fundamental insight on the connectivity and ecology of Lake Tanganyika's pelagic fish and imply that sustainable management strategies may adopt basin-scale fishing quotas.