Coastal seas are the most productive regions in the world. Surface runoff from a river is considered to be one of the most important pathways for the nutrients for primary that sustain production in coastal seas. However, in recent years, a number of studies have shown that submarine groundwater discharge (SGD) is an alternative nutrient pathway and can drive primary production in coastal seas. In Obama Bay, which is located in central Japan facing the Sea of Japan, a prominent chlorophyll-a maximum layer is formed in the bottom layer (Depth: 15-20 m) around 2-3 km offshore from the river mouth. Although the aquifer distribution in Obama Plain indicates that discharges of unconfined groundwater may induce these phytoplankton blooms, the influence of SGD on phytoplankton production is unclear. In this study, we examined seasonal and spatial changes of 222Rn (a natural groundwater tracer) in the bottom layers from the river mouth to the bay mouth, and assessed the influence of SGD on phytoplankton production in Obama Bay. Seasonal variation of 222Rn concentrations in the bottom layer were observed, with higher levels in spring and lower levels in summer. The higher 222Rn concentrations in spring were recorded at ∼20 m depth around 3 km offshore from the river mouth. Assuming that the 222Rn concentration in groundwater is constant, the seasonal variations of 222Rn concentrations in bottom waters are generated by the SGD flux. The strong influence of SGD in spring would be driven by melting of snow within the watershed of the bay. Seasonal and temporal changes in nutrients and chlorophyll-a concentrations in the bottom layer were similar to the changes in 222Rn concentration. This implies that nutrient supply through SGD is an important nutrient source for the maintenance of phytoplankton production in Obama Bay.