This study presents a novel hybrid approach that combines Graph Neural Networks (GNNs) with Reynolds-Averaged Navier Stokes (RANS) equations to enhance the accuracy of mean flow reconstruction across a range of fluid dynamics applications. Traditional purely data-driven Neural Networks (NNs) models, often struggle maintaining physical consistency. Moreover, they typically require large datasets to achieve reliable performances. The GNN framework, which naturally handles unstructured data such as complex geometries in Computational Fluid Dynamics (CFD), is here integrated with RANS equations as a physical baseline model. The methodology leverages the adjoint method, enabling the use of RANS-derived gradients as optimization terms in the GNN training process. This ensures that the learned model adheres to the governing physics, maintaining physical consistency while improving the prediction accuracy. We test our approach on multiple CFD scenarios, including cases involving generalization with respect to the Reynolds number, sparse measurements, denoising and inpainting of missing portions of the mean flow. The results demonstrate significant improvements in the accuracy of the reconstructed mean flow compared to purely data-driven models, using limited amounts of data in the training dataset. The key strengths of this study are the integration of physical laws into the training process of the GNN, and the ability to achieve high-accuracy predictions with a limited amount of data, making this approach particularly valuable for applications in fluid dynamics where data is often scarce.