In complex classification tasks, such as the classification of heterogeneous vegetation covers, the high similarity between classes can confuse the classification algorithm when assigning the correct class labels to unlabelled samples. To overcome this problem, this study aimed to develop a classification method by integrating graph-based semi-supervised learning (SSL) and an expert system (ES). The proposed method was applied to vegetation cover classification in a wetland in the Netherlands using Sentinel-2 and RapidEye imagery. Our method consisted of three main steps: object-based image analysis (OBIA), integration of SSL and an ES (SSLES), and finally, random forest classification. The generated image objects and the related features were used to construct the graph in SSL. Then, an independently developed and trained ES was used in the labelling stage of SSL to reduce the uncertainty of the process, before the final classification. Different spectral band combinations of Sentinel-2 were then considered to improve the vegetation classification. Our results show that integrating SSL and an ES can result in significantly higher classification accuracy (83.6%) compared to a supervised classifier (64.9%), SSL alone (71.8%), and ES alone (69.5%). Moreover, utilisation of all Sentinel-2 red-edge spectral band combinations yielded the highest classification accuracy (overall accuracy of 83.6% with SSLES) compared to the inclusion of other band combinations. The results of this study indicate that the utilisation of an ES in the labelling process of SSL improves the reliability of the process and provides robust performance for the classification of vegetation cover.