Water distribution system monitoring is currently carried out using advanced real-time control technologies to achieve a higher operational efficiency. Data analysis techniques can be implemented for condition estimation, which are crucial tools for managing, developing, and operating water networks using the monitored flow rate and pressure data at some network pipes and nodes. This work proposes a state estimation methodology that enables one to infer the hydraulic state of the operating speed of pumping systems from these pressure and flow measurements. The presented approach suggests using graph convolutional neural network theory linked to hydraulic models for generating a digital twin of the water system. It is validated on two benchmark hydraulic networks: the Patios-Villa del Rosario, Colombia, and the C-Town networks. The results show that the proposed model effectively predicts the state estimation in the two hydraulic networks used. The results of the evaluation metrics indicate low values of mean squared error and mean absolute error and high values of the coefficient of determination, reflecting high predictive ability and that the prediction results adequately represent the real data.