In several machine learning settings, the data of interest are well described by graphs. Examples include data pertaining to transportation networks or social networks. Further, biological data, such as proteins or molecules, lend themselves well to graph-structured descriptions. In such settings, it is desirable to design representation learning algorithms that can take into account the information captured by the underlying structure. This thesis focuses on providing new methods to ingrain geometrical information in end-to-end deep learning architectures for graphs through the use of elements from Optimal Transport theory. First, we consider the setting where the data can be described by a fixed graph. In this setting, each datapoint corresponds to a node of the graph and the edges among nodes signify their pairwise relations. We propose an autoencoder architecture that consists of a linear layer in the encoder and a novel Wasserstein barycentric layer at the decoder. Our proposed barycentric layer takes into account the underlying geometry through the diffusion distance of the graph and provides a way to obtain structure-aware, non-linear interpolations, which lead to directly interpretable node embeddings that are stable to perturbations of the graph structure. Further, the embeddings obtained with our proposed autoencoder achieve competitive or superior results compared to state-of-the-art methods in node classification tasks. Second, we consider the setting where the data consist of multiple graphs. In that setting, the graphs can be of varying size and, therefore, a global pooling operation is needed in order to obtain representations of fixed size and enable end-to-end learning with deep networks. We propose a global pooling operation that optimally preserves the statistical properties of the representations. In order to do so, we take into account the geometry of the representation space and introduce a global pooling layer that minimizes the Wasserstein distance between a graph representation and its pooled counterpart, of fixed size. This is achieved by performing a Wasserstein gradient flow with respect to the pooled representation. Our proposed method demonstrates promising results in the task of graph classification. Overall, in this thesis we provide new methods for incorporating geometrical information in end-to-end deep learning architectures for graph structured data. We believe that our proposals will contribute to the development of algorithms that learn meaningful representations and that take fully into account the geometry of the data under consideration.