An in vitro study was carried out to understand the effects of salinity shock and variation in pH on phytoplankton communities in a tropical freshwater system of the Godavari River (a major peninsular river in India). The distributions of, and variations in, phytoplankton communities were assessed by quantitative determination of their class specific marker pigments, using HPLC. Subtle changes in salinity of the freshwater by one practical salinity unit (PSU) completely removed green algae from the system and allowed the cyanobacteria to come into dominance. The cyanobacteria were found to tolerate higher osmotic stress until the salinity reached a PSU of 16. The higher salinity tolerance range of the cyanobacteria was attributed to the enhanced synthesis of zeaxanthin as protective xanthophylls against the osmotic stress. However, the effects of changing pH were not as dramatic as salinity where the green algae and the cyanobacteria from the same freshwater system showed a considerable acclimation towards the fluctuating pH. These findings are environmentally relevant to understand the likely impact of salt water intrusion and pH variation on phytoplankton communities in a tropical freshwater system.