Daya Bay, a semi-enclosed bay in the South China Sea, is well known for its aquaculture, agriculture, and tourism. In recent years, many environmental problems have emerged, such as the frequent (almost yearly) occurrence of harmful algal blooms and red tides. Therefore, investigations of submarine groundwater discharge (SGD) and associated nutrient inputs to this bay have important theoretical and practical significance to the protection of the ecological system. Such a study was conducted using short-lived radium isotopes 223Ra and 224Ra. The estimated SGD fluxes were 2.89 × 107 m3/d and 3.05 × 107 m3/d based on 223Ra and 224Ra, respectively. The average SGD flux was about 35 times greater than that of all the local rivers. The SGD-associated dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP) fluxes ranged from 1.95 × 106 to 2.06 × 106 mol/d and from 5.72 × 104 to 6.04 × 104 mol/d, respectively. The average ratio of DIN to DIP fluxes in SGD was 34, much higher than that in local rivers (about 6.46), and about twice as large as the Redfield ratio (16). Our results indicate that SGD is a significant source of nutrients to the bay and may cause frequent occurrence of harmful algal blooms. This study provides baseline data for evaluating potential environmental effects due to urbanization and economic growth in this region.