We used more than two decades (1997–2019) of satellite-estimated phytoplankton chlorophyll-a concentration (Chl-a) during September–December time intervals to discern the spatial and temporal changes of phytoplankton biomass in the Indonesian Maritime Continent (IMC) associated with different climatic events. In the IMC coastal areas (except for the northern Malacca Strait) climate changes influenced Chl-a by varying rainfall/river discharge. Chl-a declined most notably during concurrent positive Indian Ocean Dipole (IOD) and El Niño events, whereas they increased most notably during concurrent negative IOD and La Niña events. In the open ocean areas of the IMC, climate changes influenced Chl-a by varying the occurrence of upwelling and downwelling. The dominant climate mode determining Chl-a shifted from the IOD in the eastern Indian Ocean to the El Niño/Southern Oscillation (ENSO) in the western Pacific Ocean. In the eastern Indian Ocean, the impact of the IOD on Chl-a was more than one order of magnitude greater than the impact of ENSO. The results implied that low-trophic-level marine organisms such as phytoplankton, high-trophic-level marine organisms such as fish, and biogeochemical cycles in the eastern Indian Ocean of the IMC may all be more affected by the IOD than by the ENSO.