We investigate the task of missing value estimation in graphs as given by water distribution systems (WDS) based on sparse signals as a representative machine learning challenge in the domain of critical infrastructure. The underlying graphs have a comparably low node degree and high diameter, while information in the graph is globally relevant, hence graph neural networks face the challenge of long-term dependencies. We propose a specific architecture based on message passing which displays excellent results for a number of benchmark tasks in the WDS domain. Further, we investigate a multi-hop variation, which requires considerably less resources and opens an avenue towards big WDS graphs.