Wetlands are rich biological resources and support livelihood and nutritional security to a huge populace globally. In the present study, two ecologically distinct floodplain wetlands viz., Khalsi and Akaipur located in the sub-basin of Jamuna river in lower Gangetic basin, were studied for abundance, species richness and diversity indices of macro-zoobenthic communities across four seasons. The selected wetlands vary in terms of ecological regimes such as, water volume, depth, link channel, agricultural runoffs, macrophyte coverage etc. Khalsi, a seasonally open beel (wetland) that occasionally exchange water with river Jamuna during high flood, while Akaipur is a closed beel with no exchange of water. The studies indicated higher community richness in macrophyte dominated seasonally open Khalsi wetland (22species) as compared to closed Akaipur wetlands (20 species). The community abundance was higher in Khalsi (8496 nos/m2) as compared to Akaipur. Average Dominance, Simpson and Shannon diversity indices for Khalsi and Akaipur were calculated as 0.3, 0.7 & 1.5 and 0.2, 0.8 & 1.7, respectively. The community structure of wetlands revealed dominance of a single group, gastropoda (99%), followed by bivalvia (0.64%), diptera (0.27%) and oligochaeta (0.09%) in Khalsi, whereas, Akaipur depicted community structure with dominance of gastropoda (46.18%) followed by oligochaeta (41.36%), diptera (11.22%) and bivalvia (1.24%). The trophic state index (TSI) based on chlorophyll a (Chla), Secchi disc transparency and total phosphorus showed significant (p < 0.05) variations in both wetlands between different seasons. The water quality parameters were also significantly (p < 0.05) differ in both the wetlands except dissolved oxygen. The CCA components, CCA1 and CCA2 explained 27.59% and 23.95% and 39.78% and 15.26% of the species environment correlation in Akaipur and Khalsi, respectively. The distribution range of macro-zoobenthos varies 0.30–0.92 and 0.26–0.96 in Khalsi and Akaipur, respectively. The study revealed better ecosystem health of Khalsi beel in sustaining aquatic diversity while Akaipur beel is succeeding towards super eutrophic state. Thus, the present study provides baseline information on assemblage patterns and community structure of macro-zoobenthos in two important wetlands for sustainable management of the aquatic bioresources.