Coastal aquaculture ponds represented a biogeochemical hotspot in the global carbon cycle. However, there was a limited understanding of their dynamics. In this study, the eddy covariance (EC) technique was applied to quantify the net ecosystem CO2 exchange (NEE) over coastal aquaculture ponds in the Liaohe River estuary in northern China during 2020, aiming to investigate and quantify the carbon exchange characteristics of this region. The results showed that (a) a predominant “U” shaped diurnal NEE pattern throughout the year. During the sea cucumber monoculture phase, the ponds exhibited a consistent daytime carbon sink and nighttime carbon source pattern. In contrast, during the shrimp and sea cucumber polyculture phase, the ponds mostly remained in a net carbon sink state. (b) NEE was negatively correlated with photosynthetically active radiation (PAR), air temperature (Tair), and wind speed (WS), while showing a positive correlation with atmospheric pressure (AP). (c) Overall, the entire study area (complex underlying surfaces) functioned as a carbon sink in 2020, with a total net carbon sequestration of 281.533 g C·m−2. This was approximately four times greater than the restored wetlands that naturally formed from decommissioned coastal aquaculture ponds. Adjusting for surface heterogeneity revealed that the complex surfaces led to a 34.28 % underestimation of the aquaculture region's unit area carbon sequestration capacity. This study was crucial for assessing the carbon cycling and sequestration functions of coastal aquaculture pond ecosystems and provided a scientific basis for related ecological restoration projects.
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