Oikamanai Lagoon, one of lagoons in the Tokachi coastal region of Hokkaido, Japan, is a few times per year opened to the ocean by water overflow across the sand bar, which is triggered by rainfall or snowmelt runoffs of inflowing rivers. The water budget calculation for the lagoon under closed condition indicates that the net groundwater output occurs as confined groundwater output, probably to the ocean through the sand bar. The net groundwater output is then balanced mainly by river inflow. For the heat budget of the lagoon, the heat flux by the net groundwater output was estimated as an unknown factor, which was balanced by the heat flux of river inflow and a heat storage change of the lagoon. The two net groundwater outputs from the water and heat budgets exhibit the linear relationship near to the one-to-one correspondence.Hence, two unknown factors, groundwater outflow, G out , and groundwater inflow, G in , were estimated separately. As values averaged over the budget period, G out and G in were estimated at 1.04 m 3 s -1 and 0.078 m 3 s -1 (7.5% of Q Gout ), respectively. Thus, the groundwater outflow to the ocean, occupying most of groundwater output, may control the water and material cycles and the water residence time, related to the ecosystem in or around the lagoon.