Using aquatic invertebrate assemblages for bioassessment of streams and rivers is a fast and cost-effective approach to studying the impact of environmental stressors in aquatic ecosystems. The use of aquatic invertebrates is premised on their predictable responses to environmental stressors. Assemblage structure is not, however, only influenced by environment, but also neutral processes and temporal variation. This study quantified the relative roles of the environment (niche processes), space (neutral processes) and temporal factors in structuring mayfly and blackfly assemblages at family and species levels. Asymmetric eigenvector maps in conjunction with canonical redundancy analysis and variation partitioning were used to explore the relative roles of these three factors in structuring macroinvertebrate assemblages. At a species level, flow and water temperature were more important in explaining assemblage structure than at the family level. At the family level, space was more important than temporal and environmental factors. Unexplained variation at species and family level was more than 50%. This suggests (i) caution in using family-level rapid assessments to infer the role of the environment in structuring aquatic macroinvertebrate assemblages, as neutral processes are also dominant; and (ii) that the importance of stochastic processes, such as dispersal, should not be underestimated in rapid assessments.