Biomass burning is the principal tool for land clearing and a primary driver of land use change in Kalimantan (the Indonesian part of Borneo island). Biomass burning here has consumed millions of hectares of peatland and swamp forests. It also degrades air quality in Southeast Asia, perturbs the global carbon cycle, threatens ecosystem health and biodiversity, and potentially affects the global water cycle. Here we present the optimal estimate of water storage changes over Kalimantan from NASA's Gravity Recovery and Climate Experiment (GRACE). Over August 2002 to December 2014, our result shows a north-south dipole pattern in the long-term changes in terrestrial water storage (TWS) and groundwater storage (GWS). Both TWS and GWS increase in the northern part of Kalimantan, while they decrease in the southern part where fire events are the most severe. The loss rates in TWS and GWS in the southern part are 0.56 ± 0.11 cm yr−1 and 0.55 ± 0.10 cm yr−1, respectively. We use GRACE estimates, burned area, carbon emissions, and hydroclimatic data to study the relationship between biomass burning and water storage losses. The analysis shows that extensive biomass burning results in excessive evapotranspiration, which then increases long-term water storage losses in the fire-prone region of Kalimantan. Our results show the potentials of GRACE and its follow-on missions in assisting water storage and fire managements in a region with extensive biomass burning such as Kalimantan.