A hydroponic experiment has been conducted for desalination of saline water by culturing Ipomoea aquatica, Alternanthera philoxeroides and Ludwigia adscendens at 0–7 dS m−1 salinity level. Water samples were collected at 15-day interval, and the plants were harvested after 45 days. They were separated into root, stem and leaf. EC value decreased in water with increasing time for all halophytes. Root and leaf contain higher amounts of sodium as compared with those of stem. The highest accumulation of sodium was found in the root of A. philoxeroides (145.63 g kg−1); however, I. aquatic has high phytodesalination capacity (130 kg Na+ ha−1) due to high productivity than A. philoxeroides (105 kg Na+ ha−1) and L. adscendens (80 kg Na+ ha−1). Bio-concentration factors (56.10–80.29) and translocation factor values (˃ 1) indicated that these halophytes were good sodium accumulator. Sodium adsorption ration values lied between 16.8–18 at 3 dS m−1 and 20–25.5 at 5 and 7 dS m−1 showed that these halophytes improved the water quality for irrigation. Anatomical variation from microscopic cellular images illustrated that spongy mesophyll cells along with sub-stomatal cells in leaf and xylem vessels along with vacuolar sequestration might be responsible for Na accumulation in the stem of these halophytes.