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Blue carbon ecosystems are key for successful global climate change mitigation; however, they are one of the most threatened ecosystems on Earth. Thus, this study mapped the climatic and human pressures on the blue carbon ecosystems in Indonesia using multi-source spatial datasets. Data on moderate resolution imaging spectroradiometer (MODIS) ocean color standard mapped images, VIIRS (visible, infrared imaging radiometer suite) boat detection (VBD), global artificial impervious area (GAIA), MODIS surface reflectance (MOD09GA), MODIS land surface temperature (MOD11A2), and MODIS vegetation indices (MOD13A2) were combined using remote sensing and spatial analysis techniques to identify potential stresses. La Niña and El Niño phenomena caused sea surface temperature deviations to reach −0.5 to +1.2 °C. In contrast, chlorophyll-a deviations reached 22,121 to +0.5 mg m−3. Regarding fishing activities, most areas were under exploitation and relatively sustained. Concerning land activities, mangrove deforestation occurred in 560.69 km2 of the area during 2007–2016, as confirmed by a decrease of 84.9% in risk-screening environmental indicators. Overall, the potential pressures on Indonesia's blue carbon ecosystems are varied geographically. The framework of this study can be efficiently adopted to support coastal and small islands zonation planning, conservation prioritization, and marine fisheries enhancement. [ABSTRACT FROM AUTHOR]