Eutrophication is increasingly challenging the sustainability and healthy development of aquaculture. The effects of variations in nutrient dynamics remain unclear, including porewater nutrient concentrations and nutrient fluxes at the sediment-water interface (SWI), from aquaculture ponds globally, and particularly in China. In this study, temporal variation of the concentrations of nitrogen and phosphorus in porewater and their fluxes across the interface of sediment-water was investigated in the Jiulong River estuary, a subtropic estuary on the southeast coast of China. Overlying water, intact sediments, and sediment porewater were collected using sediment samplers from three shrimp ponds in June, August, and October 2015. Overlying water and sediment porewater nutrient analyses were performed using an automatic continuous flow analyzer. SONE (sediment oxygen and nutrient exchanges) incubation techniques were used to measure rates of nutrient fluxes (NO₂^--N, NO₃^--N, NH₄⁺-N, and PO₄^3--P). NO₂^--N, NO₃^--N, NH₄⁺-N, and PO₄^3--P concentrations in porewater ranged from 0.01 to 0.06, 0.06 to 0.22, 10.31 to 14.13, and 0.05 to 0.35 mg/L, respectively, with mean values of 0.04, 0.15, 11.83, and 0.17 mg/L. Higher NO₂^--N and NO₃^--N concentrations in porewater occurred during June and higher NH₄⁺-N and PO₄^3--P concentrations occurred during August. The NO₂^--N, NO₃^--N, NH₄⁺-N, and PO₄^3--P fluxes across the interface of sediment-water ranged from -2.96 to 7.60, -1.00 to 3.15, -0.79 to 4.95, and 19.23 to 91.73 mg m^-2 h^-1, respectively. The fluxes of nitrogen and phosphorus nutrients across the interface of sedimentwater showed significant temporal variation, with higher nutrient release fluxes during June and lower fluxes during October. The mean fluxes of NO₂^--N, NO₃N, and PO₄^3--P from the sediment to overlying water were (1.87±1.15), (1.58±0.52), and (1.22±0.62) mg m^-2 h^-1, respectively, indicating that the shrimp pond sediment acted as a nitrogen and phosphorus release source. Dissolved inorganic nitrogen (DIN) release dominated by excess NH₄⁺-N, and the NH₄⁺-N flux from sediment was (46.18±13.82) mg m^-2 h^-1. Pearson's correlation analysis showed that the temporal variation of nitrogen and phosphorus fluxes were significantly positively correlated with sediment temperature (P < 0.05), but significantly negatively correlated with shrimp biomass (P < 0.05). The results suggest that the temporal variation of nutrients fluxes across the sediment-water interface in shrimp ponds was controlled by the nutrient concentration gradient, sediment temperature, and the foraging and metabolic activity of shrimp. This study highlighted that the relatively high DIN (NO₂^--N and NH₄⁺-N) release from sediment during the initial and middle stages of aquaculture could be a potential pollution source in shrimp ponds, which might increase the risk of shrimp mortality.