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Background: Spatial variability of stable isotope ratios in water from River Ganges is preserved in aragonite or calcite present in otoliths and formed at equilibrium with ambient water. This technique is used in a set of long-whiskered catfish aragonite otoliths from four different locations along the course of River Ganges. Methods: Acid digestion of otolith and analysis of 13C and18O in these carbonates using an isotope ratio mass spectrometer allowed distinction of fish habitat and to provide an idea about environmental condition of water along the Ganges River. The 18O signature of otolith carbonate revealed distinct compositional trend denoting glacial water input in the upstream segment of Ganges, close to the water reservoir at Narora. However, the 13C values remained constant suggesting similar bicarbonate composition and food intake along the stream length. Results: The 18O signature in otolith from Varanasi was unexpectedly lighter and showed tendency of catfish population to migrate upstream segment of the river. The fish from the Narora location, showed the lowest 18O values, denoting signature of water derived from the melting of glacier. The heavier 18O values were seen in the stock from Kanpur. The upstream migration of fish population is indicated from the 18O values of fish otolith from Varanasi and Bhagalpur. The Varanasi location shows aberration in 18O signature in otoliths and this exists because this catfish moves to other places to avoid anthropogenic stress at this location. Conclusion: The δ18O of otolith carbonate covary with average environmental temperature recorded at individual location and serve as an important thermometry for marking environmental condition and stress in changing climatic parameters along stream length of River Ganges and its tributaries.