To evaluate biogeochemical impacts of shelf‐scale submarine groundwater discharge (SGD), the northern South China Sea (NSCS) and the East China Sea (ECS) shelf were chosen for this study. Based on a three end‐member mixing model and a Ra box model, SGD fluxes on NSCS (west and east of the Pearl River Estuary, WPRE and EPRE, respectively) and ECS shelf in winter were estimated to be 3.8–9.5 × 109, 1.4–2.2 × 109 and 0.7–2.2 ×1010 m3 d−1, respectively. Our results were equivalent to the SGD flux to the entire Mediterranean Sea, and were an order of magnitude greater than fluxes to the South Atlantic Bight. SGD associated nutrient fluxes into WPRE, EPRE and ECS were almost in the same order of magnitude, 0.2–2.4 × 103 mol m−1 d−1 for dissolved inorganic nitrogen, 1.2–9.8 mol m−1 d−1 for soluble reactive phosphorus, and 0.4–3.4 × 103 mol m−1 d−1 for dissolved silicate. Moreover, SGD delivered 1.1–2.8 × 104, 0.6–0.9 × 104, 1.7–5.1 × 104 mol m−1 d−1 dissolved inorganic carbon and 1.1–2.7 × 104, 0.5–0.8 × 104, 1.6–4.8 × 104 mol m−1 d−1 total alkalinity to WPRE, EPRE and ECS, respectively. Shelf‐scale SGD is a significant source of nutrients and carbon, and may pose great impacts on regional marine ecosystems.