Bivalves are benthic organisms inhabiting coastal marine habitats, especially estuarine tidal and mudflats. Due to their high stocking density and rich protein content, they form a major part of the artisanal fishery resource around the world. A clear partitioning in the population of bivalves, Paphia malabarica (Chemnitz, 1782), and Meretrix casta (Gmelin, 1791) in southern (Chicalim) and northern (Siridao) bank of a tropical Zuari estuary influenced by the monsoon along the Indian west coast, is evidenced. This study unravels the reasons for their partitioning in this estuary. Paphia malabarica is an exclusive inhabitant of Chicalim which has silty-sandy sediment, whereas M. casta is exclusive to Siridao, a sandy habitat. Observations showed that this segregation is facilitated by the semi-enclosed nature of habitat at Chicalim with the high amount of degraded and aged sediment organic carbon, high chlorophyll a, elemental, and biochemical components, whereas Siridao experiences the high impact of tidal currents, low sediment organic carbon, and high water column chlorophyll a. The habitat in Siridao gets exposed to UV radiation during low tide, reducing the photosynthetic oxygen production, turning the habitat to periodic anoxia indicated by differences in the TOC:TS ratio. However, such conditions may not influence M. casta, which can derive oxygen from the water column. The fatty acids specific to diatoms, dinoflagellates, higher plants, and partially degraded organic matter in the tissues of P. malabarica indicate their ability to source the food from the sediment and water column, whereas in tissues of M. casta, higher dinoflagellate-specific fatty acids followed by diatom and bacteria indicate water column-derived food. Chicalim can be considered an actively coupled benthic-pelagic habitat, and Siridao as an uncoupled habitat. Thus, the diverse flux of food particles, species-specific feeding ecology, and local hydrodynamics operating at these habitats could be the determining factors in the partitioning of the bivalves. Graphical abstract .