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In addition to monsoon-driven rainfall, the Maritime Continent (MC) is subject to heavy precipitation caused by the Madden-Julian Oscillation (MJO), a tropical convection-coupled circulation that propagates eastward from the Indian to the Pacific Ocean. This study shows that riverine runoff from MJO-driven rainfall in the western MC significantly enhances phytoplankton biomass not only in the coastal regions but as far as the nutrient-poor Banda Sea, located 1,000 km downstream of the riverine source. We present observational estimates of the chlorophyll-a concentration in the Banda Sea increasing by 20% over the winter average within an MJO life cycle. The enhancement of phytoplankton in the central Banda Sea is attributed to two coinciding MJO-triggered mechanisms: enhanced sediment loading and eastward advection of waters with high sediment and chlorophyll concentrations. Our results highlight an unexpected effect of MJO-driven rainfall on the downstream oceanic region. This finding has significant implications for the marine food chain and biogeochemical processes in the MC, given the increasing deforestation rate and projections that global warming will intensify both the frequency and strength of MJO-driven rainfall in the MC.