A three-dimensional numerical reservoir modeling of the Kotamobagu hydrothermal system was carried out. A natural state model of Kotamobagu was obtained by conducting simulations by changing parameter values of permeability, heat and mass recharges. The results of simulation were calibrated to temperature data from hot spring of Liberia and Bongkudai villages. The developed model confirmed that mass flows upward from the bottom layer to the surface, then travels laterally. The dominant mass flows through faults running northeast and to southwest. The mass from the bottom of Mt. Muayat flows to the southwest through the andesitic lava and the pumice tuff layers. Further, at the surface of Liberia and Bongkudai area, 3kg/s of mass is being discharged to the hot spring, the portion of mass flows through the fault to the southwest and continues further to the west. In the southwest area, mainly in Bakan, there is no mass discharge corresponding to related modeling blocks. Simulation results implies that the source of heat and mass discharge at the Bakan hot spring is not derived from Mt. Muayat, but from some source below sedimentary formation.