Peatland area in Indonesia was about 14.91 million ha spread out in Sumatra 6.44 million ha (43 %), in Kalimantan 4.78 million ha (32 %), and in Papua islands 3.69 million ha (25 %). In 1995, Mega Rice Project (MRP) in tropical peatland launched in Central Kalimantan, of which project failed because of knowledge gaps, especially on peatland hydrology, water management, peat subsidence, impacts of long term drainage, mechanization problems on peatland and socio-economic consequences. This paper focuses on the peatland ecosystem affected by climate change, specifically the rainfall, relating with the position of the Intertropical convergence zone (ITCZ), which has a strong influence on the seasonal variations, and the seasonal patterns of rainfall variation in different parts of Indonesia. Further, to gain a better understanding of El Niño related phenomena, we provide details of the relationship among the Southern Oscillation index (SOI), the rainfalls during dry season in Central Kalimantan, and the lowest annual groundwater level in the tropical peatlands. Kalimantan, Indonesia side of Borneo Island, has two big water storage system in peatland near costal area and humid forest of Hurt of Borneo at central mountain area. In Kalimantan, there are Main Three River Basins: the Kahayan, Mahakam, and Kapuas Rivers, which connect the Heart of Borneo with the Mountain Ranges in Borneo (Water Tower) and peatland downstream (Water Pool). As both Heart of Borneo (Water Tower) and peatland (Water Pool) interact mutually, both ecosystems destruction will induce the reduction of resilience and increase of vulnerability.
