Recent dramatic changes of freshwater systems in high latitudes will allow Submarine Fresh Groundwater Discharge (SFGD) to play a more important role in the coastal environment; especially in that SFGD will directly effect heat flux. Toyama Bay, along the central western Japan coast, is a suitable and representative case study area to estimate SFGD flux using hydrographic properties since multiple high-flow rate SFGD sites exist there. Salinities averaged over the water column (depth range 10–100 m) measured during research cruises in June 2003 and May 2005 show lower levels in the eastern than the western area in this bay. Together with monthly hydrographic properties over a 10 year period (1987–1998), the low-salinity water mass in the eastern area exists consistently but distinctly and varies systematically, as does nutrient flux, affected by SFGD more than riverine input. SFGD fluxes in June 2003 (1 × 108 m3 month−1) and May 2005 (<1 × 108 m3 month−1) were estimated using a box model, which is divided into a shallow box (0–40 m) and a deeper box (40–100 m). The monthly flux ratio between the SFGD and the river inputs is 13% in June, comparable to higher values reported in other global studies. Our results demonstrate that the box model analysis, based on hydrographic observations in coastal areas, is an efficient approach that can be used to estimate SFGD fluxes between the land and ocean.