During the past few decades, the need to intervene in underwater scenarios has grown due to the increasing necessity to perform tasks like underwater infrastructure inspection and maintenance or archaeology and geology exploration. In the last few years, the usage of Autonomous Underwater Vehicles (AUVs) has eased the workload and risks of such interventions. To automate these tasks, the AUVs have to gather the information of their surroundings, interpret it and make decisions based on it. The two main perception modalities used at close range are laser and video. In this paper, we propose the usage of a deep neural network to recognise pipes and valves in multiple underwater scenarios, using 3D RGB point cloud information provided by a stereo camera. We generate a diverse and rich dataset for the network training and testing, assessing the effect of a broad selection of hyperparameters and values. Results show F1-scores of up to 97.2% for a test set containing images with similar characteristics to the training set and up to 89.3% for a secondary test set containing images taken at different environments and with distinct characteristics from the training set. This work demonstrates the validity and robust training of the PointNet neural in underwater scenarios and its applicability for AUV intervention tasks.