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The present investigation attempted environmental characterization of two ecologically distinct oxbow lakes through zooplankton taxonomic indices using a comparative approach. These closed and seasonally open oxbow lakes are subjected to eutrophication due to different nutrient concentration and eco-hydrological characteristics. The zooplanktons are closely link with surrounding environment throughout their life cycles and change rapidly, hence act as potential indicator of eutrophication. The study examined the assemblage pattern of zooplankton community and trophic state of two ecologically distinct oxbow lakes based on eco-hydrological factors and community structure of rotifers and planktonic crustaceans seasonally over a period of 2 years. Comprehensive trophic state index (mTSI), rotifer trophic state index (mTSI ROT ) and Crustacean based indices (TSI CR ) were used to assess the degree of eutrophication. The Kruskal-Wallis test con rmed the heterogeneity of the eco-hydrological factors between the oxbow lakes. Both lakes showed transition from high meso-eutrophic to moderately eutrophic state with mTSI, mTSIrot and mTSIcr values of 54.90±11.71 and 56.95±15.64, 59.55±4.54 and 60.26±4.48, 55.79±4.76 and 60.00±4.03 in Khalsi (seasonally open) and Akaipur (closed) respectively. The Canonical Correspondence analysis (CCA) revealed water quality parameters comparison NO 3 − N, water temperature and pH have contributed more in enhancement of abundance of eutrophication indicator species Brachionus and Keratella. An overview of worldwide use of rotifer and crustacean based indices in assessment of TSI has also been synthesized. The use of these zooplankton indices to evaluate the trophic status of the ecologically distinct lakes is highly recommended for water quality assessment and management.