Heavy metal pollution in freshwater ecosystems is a serious environmental threat owing to its persistence, toxicity, and bioaccumulative characteristics. This study assesses the species-specific accumulation of heavy metals and the corresponding physiological effects in freshwater fish from the Godavari River basin. Fish samples were collected from three sampling cites: upstream, midstream, and downstream sites, representing diverse pollution gradients. Three frequently ingested species, Labeo rohita, Catla catla, and Oreochromis mossambicus, were chosen for analysis of gill, liver, and muscle tissues. The concentrations of lead (Pb), cadmium (Cd), chromium (Cr), mercury (Hg), and zinc (Zn) exhibited a consistent tissue-specific hierarchy (liver > gill > muscle). Species-specific analysis indicated greater accumulation in Oreochromis mossambicus (Pb: 3.4 ± 0.8 mg/kg; Cd: 1.5 ± 0.4 mg/kg; Zn: 68 ± 13 mg/kg in liver), succeeded by Catla catla and Labeo rohita. Spatial variation revealed that in downstream areas, the metal concentrations were much higher (Pb: 3.12 ± 0.81 mg/kg) as compare to upstream areas metal concentrations (0.92 ± 0.25 mg/kg). This indicates that people have had a big effect on the environment with respect to heavy metal water pollution. Hematological experimentation revealed a significant reduction in blood hemoglobin (11.2 ± 0.9 to 6.8 ± 1.0 g/dL) and red blood cell counts (2.8 ± 0.4 to 1.4 ± 0.2 ×10⁶/mm³), accompanied by an elevation in white blood cell counts (32 ± 8 to 104 ± 18 ×10³/mm³). Biochemical characteristics indicated increased oxidative stress, as evidenced by catalase activity rising to 96.3 ± 14.8 U/mg protein and lipid peroxidation measuring at 8.7 ± 1.9 nmol MDA/mg protein. These findings demonstrate that fish are accumulating significant toxins and experiencing considerable stress, highlighting ecological dangers and potential health risks associated with consuming fish from the Godavari River basin.