Temporal and spatial variations in Synechococcus abundance were investigated over an annual cycle (February`10–January`11) along a salinity gradient (0–35) in the tropical Zuari estuary, influenced by south-west monsoons. Synechococcus exhibited salinity preferences with phycoerythrin-rich cells at salinities >2 (Synechococcus-PEI), >20 (Synechococcus-PEII) and <1 (Synechococcus-PEIII) whereas phycocyanin-rich (Synechococcus-PC) dominant at lower salinities. Downstream stratification during monsoon caused Synechococcus group segregation in the surface and near-bottom waters. During monsoon-break and non-monsoon period stabilized waters, increased salinity, temperature, solar radiation and low rainfall favored high Synechococcus abundance whereas unstable waters, increased turbidity and low solar radiation during active monsoon lowered abundance. SYN-PC positively co-related with nitrate and phosphate and SYN-PEI with phosphate. Synechococcus contribution to phytoplankton carbon biomass ranged from 9 to 29%. In monsoonal estuaries, rainfall intensity regulates freshwater runoff which modulates the estuarine environment, creating temporal–spatial niche segregation of Synechococcus groups thereby serving as indicator organisms of the estuarine hydrodynamics.