Three species of Schoenoplectus (Reichenb.) Palla from three different sites were grown in non-aerated water conditions. Four levels of NaCl 0, 100, 200 and 300 mM were maintained in the solution medium to investigate the response of morpho-anatomical and physiological adaptations under salinity stress. S. triqueter showed optimal growth at 100 mM NaCl level and better photosynthetic response to salt stress than that recorded in other species. S. triqueter was more efficient in controlling stomatal movement. Schoenoplectus triqueter was much better adapted to salt stress than the other two Schoenoplectus species (Schoenoplectus lacustris and Schoenoplectus juncoides). Schoenoplectus triqueter also developed some structural and functional adaptive mechanisms for their survival under adverse conditions, which were retention of growth and development under high salinities, accumulation of organic osmolytes, retention of membrane integrity, retention of osmotic balance, constrained uptake of harmful ions, minimizing of water loss, lignification of parenchymatous region, succulence in terms of increased storing tissue, and reduced stomatal density. Salinity tolerance in S. lacustris were related to high accumulation of total soluble sugars and low relative membrane permeability. Root area was significantly higher in this species, having large vascular bundles and large aerenchymatous cavities. In stem, epidermal cell area and aerenchymatous cavity area was the maximum. Bracts were with large epidermal cell area, large cortical cell area and large air spaces. Moreover, stomatal area was significantly lower in this species. Leaf lamina thickness and epidermal cell area was also the maximum. Specific function features in S. juncoides for salinity tolerance were high water use efficiency, high uptake of K+ and Ca2+, and accumulation of total soluble carbohydrates. Only prominent anatomical feature in this species was significantly larger vascular bundles in leaves.