Effect of salinity stress (50-150mM Nacl) was studied in three rice varieties (Jaya, Jyoti & Korgut) commonly grown in Goankhazan fields. Damage to primary photochemistry, lipids and proteins was studied through chlorophyll fluorescence (Fv/Fm, qP, NPQ & ETR), lipid peroxidation and protein oxidation. Possible role of antioxidant system (enzymatic & non-enzymatic) in protection against given salinity stress was studied. The study showed no significant damage to photosynthetic machinery. Rice variety Jyoti, showed more lipid peroxidation indicative of damage due to salinity stress, however showed better protection through accumulation of compatible solute such as proline. Antioxidant enzymes like ascorbate and APX showed no significant increase under salinity stress. The data obtained thus showed that influence of salinity stress may vary depending upon the varieties. All the three varieties are adapted to salinity stress, but Korgut and Jyoti appeared to be more tolerant to stress.