Aquaculture ponds are potential hotspots for carbon cycling and emission of greenhouse gases (GHGs) like CO2 and CH4, but they are often poorly assessed in the global GHG budget. This study determined the temporal variations of CO2 and CH4 concentrations and diffusive fluxes and their environmental drivers in coastal aquaculture ponds in southeastern China over a five-year period (2017-2021). The findings indicated that CH4 flux from aquaculture ponds fluctuated markedly year-to-year, and CO2 flux varied between positive and negative between years. The coefficient of inter-annual variation of CO2 and CH4 diffusive fluxes was 168% and 127%, respectively, highlighting the importance of long-term observations to improve GHG assessment from aquaculture ponds. In addition to chlorophyll-a and dissolved oxygen as the common environmental drivers, CO2 was further regulated by total dissolved phosphorus and CH4 by dissolved organic carbon. Feed conversion ratio correlated positively with both CO2 and CH4 concentrations and fluxes, showing that unconsumed feeds fueled microbial GHG production. A linear regression based on binned (averaged) monthly CO2 diffusive flux data, calculated from CO2 concentrations, can be used to estimate CH4 diffusive flux with a fair degree of confidence (r2 = 0.66; p < 0.001). This algorithm provides a simple and practical way to assess the total carbon diffusive flux from aquaculture ponds. Overall, this study provides new insights into mitigating the carbon footprint of aquaculture production and assessing the impact of aquaculture ponds on the regional and global scales.