Submarine groundwater discharge (SGD) plays a crucial role in nutrient dynamics and eutrophication status of the typical estuarine ecosystems, which are hotspots for groundwater-borne nutrient and are sensitive to aquaculture activities. To evaluate the significant role of SGD in regulating nutrient dynamics in an aquaculture estuary, a radium mass balance model combined biological feeding experiment was carried out in the present study. The results demonstrated that SGD fluxes were estimated to be 15.9 ± 9.41 cm d−1, 18.1 ± 8.51 cm d−1, and 23.0 ± 13.7 cm d−1 during July 2019, October 2019 and April 2021, and the SGD-driven dissolved inorganic/organic nutrient fluxes were 0.6–3.1-fold, 0.2–0.9-fold and 0.4–29-fold higher than those of riverine input, respectively. Seasonal variabilities of SGD rates indicated that saline SGD is dominated and is primarily modified by the oceanic forcing stimulated by tidal and wave dynamics. The contrasting conditions between bottom-up (groundwater- and river-derived nutrient fluxes) and top-down (nutrient responses in estuarine waters), showed the significance of seasonal differences in the biochemical mechanisms and aquaculture effects of modifying nitrogen dynamics. Dissimilatory nitrate reduction to ammonium and nitrification were responsible for the contrasting NOx− (NO2− and NO3−) and NH4+ conditions in July and October, respectively, and these factors jointly regulated NOx− and NH4+ in April. Dissolved organic nitrogen (DON) was the predominant component among the three seasons, except for DON degeneration in October, and it increased due to NH4+ assimilation by the phytoplankton community. These findings indicated that biochemical transformation has potential ramifications for the dynamics of SGD-driven nutrients and the management in marine aquaculture ecosystems.