Twelve years of remotely sensed all-sat merged chlorophyll-a concentration unveils strong signatures of chlorophyll-a blooms along the south Java coast. An unprecedented three-times increase in chlorophyll-a concentration is significantly observed along the south Java coast during the southeast monsoon (June–October) than the northwest monsoon (December–April). The multiple regression analysis of dynamic factors evidently indicates that seasonal upwelling is predominantly controlled by the seasonally evolving coastal eddies associated with the seasonally reversing south Java coastal currents (SJCC) and Ekman mass transport (EMT), followed by the relative roles of sea surface temperature (SST) and wind stress curl. The eddy-induced upwelling and EMT-induced coastal upwelling lead to chlorophyll-a blooms during southeast monsoon, well-supported by the entrainment of cold and saline waters (thermocline doming) with low spiciness. On the other hand, the coastal eddies associated with SJCC and SST anomalies play a significant role in modulating the interannual surface chlorophyll-a variability in the domain. Intense chlorophyll-a blooms are observed during the positive IOD years, whereas the least chlorophyll-a concentration is observed during the negative IOD years. The unprecedentedly least chlorophyll-a concentrations during 2010 and 2016 are attributed to the intense and prolonged surface marine heatwaves.