This study assessed phytoplankton community composition variation under two discrete salinity intrusion rate experiments. Experiment 1 simulated salinization under short-term, natural tidally induced rates of salinity change typical of the Mekong Delta, Vietnam (0‰ to 30‰ in 6 hours), while Experiment 2 simulated salinization under a longer, more gradual rate of salinity change (0‰ to 30‰ at 5‰ increase per week). Phytoplankton community composition was, overall, more abundant following prolonged salinity change (Experiment 2) than rapid, tidally-induced salinity change (Experiment 1). Under both experimental conditions phytoplankton species number and density varied with changes in salinity, indicating a strong effect of salinity regardless of  its rate of change. At the end of the salinity acclimation, Cyanobacteria , Chlorophyta, Euglenophyta and Bacillariophyta were all most abundant  at a salinity of 5‰ after a short-term tidally simulated change in salinity, but with a longer, more gradual change in salinity, the abundance of different groups varied with salinity;  With a longer, more gradual change in salinity, Chlorophyta was most abundant at 5‰-10‰ salinity, while Cyanobacteria, Euglenophyta and Bacillariophyta were all most abundant at a salinity of 5‰. The species composition in treatments of less than 10‰ had high similarity with the freshwater environment while treatments of 30‰ (Experiment 1) and 25‰ (Experiment 2) had high similarity with the natural seawater environment. This study demonstrates the utility of mesocosm experiments for understanding phytoplankton community composition variation in natural aquatic ecosystems under rapid and prolonged saline intrusion rates and predicting associated impacts on food webs in natural water bodies and aquaculture systems.