In this paper we introduce a novel machine learning-based fully automatic approach for the semantic analysis and documentation of masonry wall images, performing in parallel automatic detection and virtual completion of occluded or damaged wall regions, and brick segmentation leading to an accurate model of the wall structure. For this purpose, we propose a four-stage algorithm which comprises three interacting deep neural networks and a watershed transform-based brick outline extraction step. At the beginning, a U-Net-based sub-network performs initial wall segmentation into brick, mortar and occluded regions, which is followed by a two-stage adversarial inpainting model. The first adversarial network predicts the schematic mortar-brick pattern of the occluded areas based on the observed wall structure, providing in itself valuable structural information for archeological and architectural applications. The second adversarial network predicts the pixels’ color values yielding a realistic visual experience for the observer. Finally, using the neural network outputs as markers in a watershed-based segmentation process, we generate the accurate contours of the individual bricks, both in the originally visible and in the artificially inpainted wall regions. Note that while the first three stages implement a sequential pipeline, they interact through dependencies of their loss functions admitting the consideration of hidden feature dependencies between the different network components. For training and testing the network a new dataset has been created, and an extensive qualitative and quantitative evaluation versus the state-of-the-art is given. The experiments confirmed that the proposed method outperforms the reference techniques both in terms of wall structure estimation and regarding the visual quality of the inpainting step, moreover it can be robustly used for various different masonry wall types.