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Coastal aquaculture monitoring is vital for sustainable offshore aquaculture management. However, the dense distribution and various sizes of aquacultures make it challenging to accurately extract the boundaries of aquaculture ponds. In this study, we develop a novel combined framework that integrates UNet++ with a marker-controlled watershed segmentation strategy to facilitate aquaculture boundary extraction from fully polarimetric GaoFen-3 SAR imagery. First, four polarimetric decomposition algorithms were applied to extract 13 polarimetric scattering features. Together with the nine other polarisation and texture features, a total of 22 polarimetric features were then extracted, among which four were optimised according to the separability index. Subsequently, to reduce the “adhesion” phenomenon and separate adjacent and even adhering ponds into individual aquaculture units, two UNet++ subnetworks were utilised to construct the marker and foreground functions, the results of which were then used in the marker-controlled watershed algorithm to obtain refined aquaculture results. A multiclass segmentation strategy that divides the intermediate markers into three categories (aquaculture, background and dikes) was applied to the marker function. In addition, a boundary patch refinement postprocessing strategy was applied to the two subnetworks to extract and repair the complex/error-prone boundaries of the aquaculture ponds, followed by a morphological operation that was conducted for label augmentation. An experimental investigation performed to extract individual aquacultures in the Yancheng Coastal Wetlands indicated that the crucial features for aquacultures are Shannon entropy (SE), the intensity component of SE (SE_I) and the corresponding mean texture features (Mean_SE and Mean_SE_I). When the optimal features were introduced, our proposed method performed better than standard UNet++ in aquaculture extraction, achieving improvements of 1.8%, 3.2%, 21.7% and 12.1% in F1, IoU, MR and insF1, respectively. The experimental results indicate that the proposed method can handle the adhesion of both adjacent objects and unclear boundaries effectively and capture clear and refined aquaculture boundaries.