Submarine groundwater discharge (SGD) and associated nutrient have long been received insufficient attention in the aquaculture areas of Lianjiang, East China Sea. In this study, we used 224Ra mass balance model to evaluate the importance of SGD in the aquaculture areas of Lianjiang in different seasons. The results showed that SGD fluxes were 0.14 ± 0.070 m3 m−2 d−1 in July and 0.077 ± 0.040 m3 m−2 d−1 in October 2019, which corresponded to approximately 22% and 32% of the river discharge, respectively. Nevertheless, the dissolved inorganic nitrogen (DIN) and phosphorus (DIP) fluxes contributed by SGD over total nutrient inputs were approximately 58% and 73%, respectively in July, 11% and 33%, respectively in October 2019. The ratio of DIN to DIP in seawater was slightly higher than that derived from SGD in July and significantly lower than that derived from the river and SGD in October, which was prone to profound modulated by shellfish (e.g., clam Ruditapes philippinarum and Sinonovacula constricta) and nori (e.g., Pyropia haitanensis) that selectively acquire nitrogen and phosphorous, suggesting that SGD could affect the nutrient structure and aquaculture activities in Lianjiang. Moreover, the new primary production via SGD yielded (2.47 ± 1.32) × 103 mg C m−2 d−1 in July and (3.52 ± 1.76) × 102 mg C m−2 d−1 in October 2019, which were approximately 8–25% and 10–31% of the production in the entire study area. These meaningful discoveries indicated that SGD and associated nutrient are the predominant regulator of nutrient and aquaculture structure under significant seasonal differences.