Hierarchical graphs (e.g. file system browsers and preference trees) represent objects (e.g. files and folders) as graph nodes and relations between them (e.g. sub‐folder relations) as lines. We investigated the temporal organisation of two processes that are necessary for comprehending such graphs—search for the graph nodes and reasoning about their relation. We tracked eye movements to change graphs while participants interpreted them. In Experiment 1, we masked the graph at a time when search processes had finished but reasoning was hypothetically ongoing. We observed a dramatic deterioration in comprehension compared with unmasked graphs. In Experiment 2, we changed the relation between critical graph nodes after search for them had finished, unbeknownst to participants. Participants mostly based their response on the graph as presented after the change. These results suggest that comprehension processes are organised in a sequential manner, an observation that can potentially be applied to the interactive presentation of graphs. Copyright © 2014 John Wiley & Sons, Ltd.