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Small island ecosystems and their inhabitants face a significant threat from global warming, jeopardizing their sustainability. These communities are particularly vulnerable to the impact of climate change, as they heavily rely on natural resources for their livelihoods and are more vulnerable than mainland regions. Therefore, it is essential to take urgent action to address the challenges small island states face and promote their resilience in the face of climate change. To preserve the coastal ecosystems in Karimunjawa Islands, Indonesia, this study proposes an alternative spatial plan through micro-zonation analysis. The study conducted literature reviews and field surveys to collect data and develop recommendations for the current spatial plans through spatial, descriptive statistics, and comparative analysis. The findings show that the sea surface temperatures of Karimunjawa and Kemujan Island have increased by 1-2 ℃. Stress levels were found for coral reefs at the bleaching warning position for all Karimunjawa Island marine areas, including Kemujan Island. Legon Lele and Tanjung Gelam were found to have suspended sediment traces and indications of heavy metal contamination, making them the research focus. The Karimunjawa micro-zonation boundaries were obtained, especially in the Legon Lele and Tanjung Gelam areas, with an area of 640.63 and 817.45 ha, respectively. The proposed micro-zonation for Karimunjawa National Park refers to watershed-sedimentary cells, making it an example of implementing integrated coastal management (ICM) spatial boundaries in Karimunjawa and other nations. By applying this micro-zonation, coastal ecosystem rehabilitation efforts can be carried out precisely., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)