Mangroves, which are vulnerable to natural threats and human activities on small islands in the tropics, play an essential role as carbon sinks, helping to mitigate climate change. In this study, we discussed the effect of natural factors on mangrove sustainability by analyzing the impact of rainfall, land surface temperature (LST), and tidal inundation on the greenness of mangroves in Karimunjawa National Park (KNP), Indonesia. We used Sentinel-2 image data to obtain the normalized difference vegetation index (NDVI) and normalized difference moisture index (NDMI) during the dry season to determine the effect of inundation on mangrove greenness and soil moisture. The tidal inundation area was calculated using topographic data from the KNP and tidal observations from the area adjacent to it. Unmanned autonomous vehicles and topographic data were used to estimate mangrove canopy height. We also calculated mangrove greenness phenology and compared it to rainfall from satellite data from 2019–2021. Results show that the intertidal area is dominated by taller mangroves and has higher NDVI and NDMI values than non-intertidal areas. We also observed that mangroves in intertidal areas are mostly evergreen, and optimum greenness in KNP occurs from February to October, with maximum greenness in July. Cross-correlation analysis suggests that high rainfall affects NDVI, with peak greenness occurring three months after high rainfall. The LST and NDVI cross-correlation showed no time lag. This suggests that LST was not the main factor controlling mangrove greenness, suggesting tides and rainfall influence mangrove greenness. The mangroves are also vulnerable to climate variability and change, which limits rainfall. However, sea-level rise due to climate change might positively impact mangrove greenness.