The presence of substructure in galaxy groups and clusters is believed to be a sign of recent galaxy accretion and can be used to probe not only the assembly history of these structures, but also the evolution of their member galaxies. Using the Dressler–Shectman (DS) test, we study substructure in a sample of intermediate-redshift (z∼ 0.4) galaxy groups from the Group Environment and Evolution Collaboration (GEEC) group catalogue. We find that four of the 15 rich GEEC groups, with an average velocity dispersion of ∼525 km s−1, are identified as having significant substructure. The identified regions of localized substructure lie on the group outskirts and in some cases appear to be infalling. In a comparison of galaxy properties for the members of groups with and without substructure, we find that the groups with substructure have a significantly higher fraction of blue and star-forming galaxies and a parent colour distribution that resembles that of the field population rather than the overall group population. In addition, we observe correlations between the detection of substructure and other dynamical measures, such as velocity distributions and velocity dispersion profiles. Based on this analysis, we conclude that some galaxy groups contain significant substructure and that these groups have properties and galaxy populations that differ from groups with no detected substructure. These results indicate that the substructure galaxies, which lie preferentially on the group outskirts and could be infalling, do not exhibit signs of environmental effects, since little or no star formation quenching is observed in these systems.