In this study, we used a 224Ra mass balance model to evaluate the importance of submarine groundwater discharge (SGD) for the budgets of biogenic elements in two major Chinese estuaries: the Pearl River Estuary (PRE) and the Changjiang River Estuary (CRE). The apparent water age in the PRE was estimated to be 4.8 ± 1.1 days in the dry season and 1.8 ± 0.6 days in the wet season using a physical model based on the tidal prism. In the dry season, the water age in the CRE was estimated to be 11.7 ± 3.0 days using the 224Ra/223Ra activities ratios apparent age model. By applying the 224Ra mass balance model, we obtained calculations of the SGD flow in the PRE of (4.5–10) × 108 m3 d−1 (0.23–0.50 m3 m−2 d−1) and (1.2–2.7) × 108 m3 d−1 (0.06–0.14 m3 m−2 d−1) in the dry season and wet season, respectively, and the estimated SGD flux was (4.6–11) × 109 m3 d−1 (0.18–0.45 m3 m−2 d−1) in the dry season of the CRE. In comparison with the nutrient fluxes from the rivers, the SGD-derived nutrient fluxes may play a vital role in controlling the nutrient budgets and stoichiometry in the study areas. The large amount of dissolved inorganic nitrogen and phosphorus fluxes together with high N: P ratios into the PRE and CRE would potentially contribute to eutrophication and the occurrence of red tides along the adjacent waters. Display omitted •Physical model and 224Ra/223Ra were used to estimate water ages in the Pearl River Estuary and Changjiang River Estuary.•Submarine groundwater discharge (SGD) was evaluated using a 224Ra mass balance model.•SGD is important for hydrology and nutrient budgets in the Pearl River Estuary and Changjiang River Estuary.