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• High concentrations of PCBs were found at locations near Jinja Municipality.• The PCB and HCH levels were low to moderate compared to other locations worldwide.• The fish from the Napoleon Gulf was fit for consumption in regard to PCBs and HCHs.• The ratios of α-/γ-HCH were low suggesting past input of lindane. a b s t r a c t a r t i c l e i n f o Polychlorinated biphenyls (PCBs) and hexachlorocyclohexanes (HCHs) were analyzed in surface sediments (b30 cm depth) and two fish species: Nile perch (Lates niloticus) and Nile tilapia (Oreochromis niloticus). The samples were collected from the Napoleon Gulf on the northern shore of Lake Victoria. The analysis was done using a gas chromatograph (GC) coupled to a high resolution mass spectrometer for PCBs and a GC equipped with an electron capture detector for HCHs. Total (Σ) PCBs in the muscles of fish varied widely with mean values ranging from 41 to 670 pg g −1 lipid weight (lw). The PCB levels in L. niloticus were significantly greater than those in O. niloticus. The large variability observed in the data was attributed to differences in feeding habits and trophic levels. While O. niloticus is a filter-eating fish species feeding mainly on phytoplankton and zooplankton, L. niloticus have predatory feeding behaviors and prefer a diet of live fish and, therefore, are more prone to bioaccumulate contaminants. The mean PCB concentrations in the sediments varied from 362 to 848 pg g −1 dry weight. Variations in PCB levels were observed from one study site to another, this was attributed to the nature and particle size of the sediments. HCH isomers were detected in fish at mean concentrations of up to 45,900 pg g −1 lw. The PCB and HCH concentrations were lower than those from previous studies elsewhere in literature and were below the maximum residue limits set by the European Commission and FAO/WHO Codex Alimentarius Commission, implying that the fish was fit for human consumption.