The Indian Sundarbans is a highly vulnerable ecosystem exposed to climate change with salinity intrusion, increasing cyclones as well as anomalies in rainfall and temperature that create an adverse impact on the physiology of resident and migratory fishes. Changes in the density and morphology of chloride cells are essential adaptive characters in response to varying salt level in the environment. Therefore, the present study attempts to compare the morphology, localization and abundance of chloride cells in the fishes representing different migratory guilds of the Matla River estuary of Sundarbans. The variations in the respective expression of the Na+K+ATPase α1 protein in chloride cells could comprehend the physiological adjustments across different migratory fish guilds. As observed in the present study, the chloride cells were concentrated at the base of the secondary lamellae in estuarine fishes whereas they occupied the interlamellar position for freshwater, air-breathing and amphidromous fishes, with the variations of such localizations being very prominent. The mean length of chloride cells was significantly higher in estuarine migratory fishes as compared to the amphidromous and freshwater species. However, the abundance of these cells was significantly higher in the estuarine migratory species and freshwater Labeo rohita compared to amphidromous ones. The combined patterns in abundance and immunolocalization of Na+K+ATPase in chloride cells illustrated a unique pattern and functional plasticity in the ion-transporting epithelia of the freshwater and estuarine fishes with important mechanisms of osmoregulatory ability. Hence, the study provides a clue to how osmoregulatory adjustments could be linked to the adaptive strategies in the ichthyofaunal communities of a mangrove estuary as vulnerable as Sundarban. Further studies may facilitate a better understanding of the fish physiology in formulating efficient management efforts to conserve aquatic resources in such vulnerable environments with a view to a certain climate change.