Water quality deterioration can adversely affect the long-term sustainability of aquaculture industry. Understanding the processes of nutrient regeneration and uptake is important for improving water quality and the overall ecosystem health of aquaculture system. In spite of the importance of dissolved nutrients (DOC, DIC, N-NOx-, N-NH4+, and P-PO43-) in governing water quality and ecosystem functioning, the spatiotemporal variations in the production and uptake of dissolved nutrients in aquaculture ponds is still poorly understood. In this study, the nutrient production and uptake rates in the overlying water were quantified among different shrimp growth stages in the aquaculture ponds in the Min River Estuary (MRE) and Jiulong River Estuary (JRE), southeast China. Significant differences in the nutrient production and uptake rates in the overlying water were observed among the three growth stages and two estuaries. The temporal variations of DOC and DIC production rates in both estuarine ponds closely followed the seasonal cycle of temperature, while the difference in DOC and DIC production rates between the two estuaries was likely caused by differences in water salinity. The changes in the production and uptake rates of dissolved inorganic nitrogen (N-NOx- and N-NH4+) and P-PO43- in the water column over time were partly related to the interactions between thermal conditions and phytoplankton biomass (e.g., chlorophyll a concentrations) in the ponds. Our results demonstrate the complex dynamics and environmental risk of dissolved nutrients in subtropical shrimp ponds, and call for a more effective management of nutrient-laden wastewater in safeguarding the long-term sustainability of aquaculture production.