Toxicity studies in the aquatic ecosystem have shown that petrol and its product have adverse effects on aquatic biota. They are able to easily absorb these toxic substances into their bodies from sediment, water or even food items that are contaminated, thus impacting the food chain. In this study, water, sediment and fish (Heterotis niloticus) from the Epe Lagoon were investigated for the presence of BTEX (benzene, toluene, ethylbenzene and the three xylene isomers m, o and p-xylenes), and PAHs using GC-MS. Total concentration of BTEX in sediment and water was respectively 32.37 AE 1.07 μg/g, 49.86 AE 7.30 μg/L; while total concentration of BTEX in fish liver and intestine was 33.75 AE 10.09 and 40.16 AE 9.64 μg/g respectively. Benzene, 1,2-Dichlorobenzene and 1,3-Dichlorobenzene components of BTEX were not detected in both sediment and water. Total concentration of PAH in sediment and water was 7.46 AE 1.73 μg/g and 19.33 AE 1.31 μg/L respectively. Total PAHs concentration in liver and fish intestine was 141.23 AE 5.89 and 173.34 AE 4.677 μg/g respectively. Majority of the PAHs congeners were found to be higher than the acceptable limits. Findings from this study shows the need for continuous monitoring of our natural waters as the present situation portends a potential concern for ecological risk.