The Koggala lagoon is a coastal wetland affected by a major oil spill and other anthropogenic pollution sources. In this study, gill and liver histological alterations and polycyclic aromatic hydrocarbon (PAH) exposure indicative bile fluorescence patterns of the fish species inhabiting the lagoon were examined in order to explore the potential biological impacts. Fixed wavelength fluorescence patterns in the bile of Mugil cephalus, Lutjanus russellii and Etroplus suratensis showed bioavailability of naphthalene type-, phenanthrene type-, pyrene type- and benzo(a)pyrene type- metabolites indicating recent exposure of the fishes to petrogenic and pyrogenic PAHs. Histological analysis revealed the occurrence of prominent gill and liver lesions, especially in the tissues of M cephalus and L. russellii. Of the fish species examined, which included 43 individual fishes, the liver tissues of M cephalus (two fish) and L. russellii (one fish) displayed foci of hepatocellular alterations with nodular hyperplasia. This is the first record on pre-tumor type hepatic lesions seen in fishes living in Sri Lankan waters. This study provides scientific evidence for the biological impacts on the resident fishes in the Koggala lagoon, and calls for further research on the impacts of coastal water pollution in Sri Lanka and potential management strategies.