Certifying the robustness of a graph-based machine learning model poses a critical challenge for safety. Current robustness certificates for graph classifiers guarantee output invariance with respect to the total number of node pair flips (edge addition or edge deletion), which amounts to an $l_{0}$ ball centred on the adjacency matrix. Although theoretically attractive, this type of isotropic structural noise can be too restrictive in practical scenarios where some node pairs are more critical than others in determining the classifier's output. The certificate, in this case, gives a pessimistic depiction of the robustness of the graph model. To tackle this issue, we develop a randomised smoothing method based on adding an anisotropic noise distribution to the input graph structure. We show that our process generates structural-aware certificates for our classifiers, whereby the magnitude of robustness certificates can vary across different pre-defined structures of the graph. We demonstrate the benefits of these certificates in both synthetic and real-world experiments.