The effect of neap-spring transition on the spatial and temporal changes in the cell size distribution of different phytoplankton species and their size-based habitats distribution were investigated in the highly turbid macrotidal Chikugo River estuary, Japan in 2021. The estuarine mixing changed from stratified to well-mixed over the transition from neap to spring tides and saltwater (1-5) intruded until 17 km with negligible effect from river discharge. The suspended sediment concentration (SSC) was low (<40 mg L^-1) during neap tide and highest (1000 mg L^-1) during spring tide associated with strong mixing, which led to the formation of an estuarine turbidity maximum (ETM) zone between 8 and 12 km. A total of 159 phytoplankton species were identified in the estuary and are classified into seven groups. The diatoms (freshwater and marine habitats) were found as significant groups (79-86 %). Principal component analysis (PCA) results showed that salinity (p < 0.05) and mixing (p < 0.05) were the major controlling factors in the phytoplankton habitats distribution. The diatoms abundance started to increase from neap tide and reached the maximum abundance (174.714 cells/mL) two days after neap tide, then decreased towards spring tide (69.257 cells/mL). Additionally, the cell sizes of dominant diatoms species (Skeletonema costatum and Nitzschia acicularis) increased from neap to intermediate tides and continued increasing until the spring tide. Spatially, the abundance of diatoms was lower in the middle estuary (67-86 cells/mL) than in other parts because of ETM formation, although larger size distribution occurred. This study concludes that the abundance and size distribution of phytoplankton are influenced by estuarine mixing, and the neap-spring transition phase is more essential for phytoplankton growth than individual neap and spring tides in tide-dominated estuaries. Furthermore, size-increasing patterns play an important role in sustaining their survival strategy under the strong turbulent conditions in addition to saltwater intrusion and ETM.