Seasonal and neap-spring tidal changes in estuarine physical variables and their effect on the phytoplankton distribution in the macrotidal Tanintharyi River estuary (TRE), Myanmar were studied in 2019. During the dry season, the saltwater intrudes upstream while only until the mid-estuary during the wet season due to the hindering of saltwater by the strong river flow. The turbidity variations driven by enhanced mixing and neap-spring transition influenced the light required for phytoplankton growth during both seasons. The diversity index was higher (2.57–3.07) in the dry season with low evenness (0.64–0.79) compared to the low diversity index (2.16–2.73) with high evenness (0.75–0.90) in the wet season. The peak diatom density was observed under low turbidity (6 FTU) and a salinity of 25, and their distribution were correlated positively with salinity, mean light intensity in the mixed layer (Im) and euphotic depth (Ze) while negatively with light attenuation (K) and turbidity. Among diatoms species, Thalassionema frauenfeldii, Thalassionema nitzschioides and Pseudonitzschia seriata were found as dominant species (positively correlated with salinity and Im whereas negatively with turbidity and K) during the dry season whereas Thalassiosira eccentrica and Coscinodiscus granii were dominant with low salinity in the wet season. The dinoflagellates were more sensitive to strong mixing condition than diatoms and their distribution were positively influenced by Im and Ze. Therefore, the neap-spring tidal and seasonal variations in saltwater intrusion, mixing, turbidity, and light availability are the major factors that maintained the phytoplankton diversity in the tropical TRE.