Nutrients supplied from submarine groundwater discharge (SGD) are generally thought to enhance primary production in coastal seas. However, there is little evidence for a direct association between SGD and phytoplankton primary productivity. To elucidate the response of in situ primary productivity to SGD, we conducted comparative experiments at 3 coastal sites in Japan with different SGD types (Site A: Obama Bay; Site B: coast along the western foot of Mt. Chokai; Site C: Beppu Bay) during the summers of 2013-2015. At Site A, which is characterized by seepage-type SGD, we found a significant positive relationship between in situ primary productivity and Rn-222 concentration. This was likely driven by nutrient-limited water column conditions. On the other hand, at the volcanic coastal Sites B and C, which are dominated by spring-type SGD, no clear relationships between in situ primary productivity and 222Rn concentration were found. Although significant relationships between nutrient concentrations and 222Rn concentration suggest that SGD acts as a primary nutrient source in these regions, the non-trivial influence of light availability complicates those relationships. Furthermore, lower biomass-specific primary productivity around submarine springs at both sites suggests that submarine springs have negative impacts on phytoplankton growth rates around vent sites, possibly due to changes in local environmental conditions. Our study clarified that the mechanism by which SGD affects phytoplankton production differs from one ecosystem to another because of variable hydrogeographical properties, such as the type of groundwater discharge (i.e. spring or seepage).