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Globally, stable isotopic methods are rapidly being employed in food web studies to quantify the relative proportions of diverse primary carbon sources in an animal diet. Tropical estuarine ecosystems, one of the vital marine habitats, harbor complex food webs due to the multiplicity of habitats and resources. The complex system of inputs and exchanges of organic matter sometimes complicate identification of the carbon sources that support the higher trophic levels. To assess the primary food sources of four abundant amphipod species in the anthropogenically influenced upper Vashishti estuary, Carbon and Nitrogen stable isotopes were employed. Seasonal variations were significant for δ13C and δ15N of suspended particulate organic matter (SPOM) and also for δ13C of sediment organic matter (SOM), but not for the isotopic values of individual amphipod species. Significant variations in the δ13C and δ15N values between amphipods suggested species-specific diets. Mixing model output indicated discrepancies in seasonal variations of food preferences between species. Trophic level values of all amphipod species indicated seasonality with lower values during post-monsoon. The low δ15N values of SPOM, SOM, and amphipod species were possibly due to the anthropogenic input of nitrogen in the estuary. [ABSTRACT FROM AUTHOR]