The Eastern Indonesian waters are significant in influencing the global climate system and oceanic connectivity. However, the Indonesian Through Flow (ITF) facilitates the movement of waters from the Pacific Ocean to the Indian Ocean. This flow vertically mixes water masses in the Eastern regions, leading to the concentration of phytoplankton. In addition, the distribution of phytoplankton, indicative of chlorophyll-a concentration, is influenced by upwelling and downwelling phenomena. Chlorophyll-a, responsible for capturing carbon and producing oxygen in marine ecosystems, is important in regulating climate change. Moreover, oceanographic conditions play a significant role in the dispersion of chlorophyll-a concentration. Therefore, this study adopted ocean colour remote sensing technology to assess chlorophyll-a distribution. Monthly ocean colour data was collected by the multi-temporal Sentinel-3 Ocean and Land Colour Instrument (OLCI). The analysis output included chlorophyll-a concentration associated with currents and the El Nino Southern Oscillation (ENSO). Data processing using the Case-2 Regional Coast Colour (C2RCC) processor resulted in an average chlorophyll-a concentration in the Eastern Indonesian waters ranging from 0.16 to 0.52. The results showed higher chlorophyll-a levels during the southeast monsoon (July to September) and lower levels during the northwest monsoon (January to March).