In recent years closed and seasonally open oxbow lakes and river floodplains are subjected to eutrophication due to disconnection from river that compromises the hydro-ecological functions. This requires systematic studies to assess the ecological health of the water bodies using different indices and suggest appropriate strategies to manage the resources. The zooplanktons are closely link with surrounding environment throughout their life cycles and change rapidly in their growth and population when changes occurs in the surrounding, hence act as potential indicator of eutrophication. The present study examined the assemblage pattern of zooplankton community and trophic state of two ecologically distinct oxbow lakes based on eco-hydrological characteristics and community structure of rotifers and planktonic crustaceans seasonally over a period of 2 years. Comprehensive trophic state index (mTSI), rotifer trophic state index (mTSIROT) and Crustacean based indices (TSICR) were used to assess the degree of eutrophication. The Kruskal-Wallis test confirmed the heterogeneity of the eco-hydrological factors between the oxbow lakes. A total of 68 zooplankton species were identified of which rotifers (69%), cladocerans (18%), copepods (3%), ostacods (3%) and protozoans (7%). Seasonal fluctuation of relative abundance and frequency of species in both lakes have been well presented. 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 NO3-N, water temperature and pH have contributed more in enhancement of abundance of eutrophication indicator species Brachionus and Keratella. The TSIs values indicated a prompt aquaculture fisheries management measures like stocking of planktivorous fish (Labeo catla and Puntius sp.) for both the lakes before they reach in plunged state at which their restoration might become a challenge. 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. Based on this study strategies could be developed to plan and manage floodplain oxbow lakes for fisheries enhancement programme as well as as conservation of biodiversity.