The histological and functional characteristics of fish gills are crucial indicators of environmental quality and are widely utilized as bioindicators for ecological monitoring. This study examined the gill histology of Cyprinus carpio and Liza abu to assess the ecological health of the Shatt al- Arab River across four sites: Site 1 (Haratha Electric Power); Site 2 (Najebia Electric Power); Site 3 (Kandac Canal); and Site 4 (North Shatt Al Arab). Site 4, considered as a control station, exhibited good environmental conditions, while Sites 1, 2, and 3 were contaminated with human and industrial wastes. At Sites 1, 2, and 3, the gills of both fish species showed significant damage, including epithelial lifting, necrosis, degeneration, and congested blood vessels. Furthermore, there were disturbances in osmoregulation, as indicated by altered concentrations of sodium (Na+), potassium (K+), and calcium (Ca2+) ions in the gills, as well as an increase in gill chloride cells. Genetic mutations were also observed, evident from the presence of micronuclei in the red blood cells. In contrast, no apparent gill damage was observed at Site 4. Our results confirmed that L. abu was more sensitive to aquatic pollution than C. carpio. Overall, the findings suggest that gill histological markers can be effectively used as bioindicators for evaluating the environmental impact on river ecosystems.