Assessing and explaining patterns of biodiversity is crucial to achieving conservation goals in freshwater systems. While much information on freshwater insect biodiversity comes from biomonitoring, these programs are only beginning to consider the effect of group-level trait variation on compositional variation. We sought to test the hypothesis that dispersal ability is an important factor driving variation in aquatic insect communities. Specifically, we predict that a group with high dispersal ability (Odonata) will show less compositional variation than a group with low dispersal ability (Trichoptera). We present results of a multi-habitat assessment of Odonata and Trichoptera diversity conducted at 44 sites across three fifth-order watersheds in New Brunswick, Canada. At each site, a suite of environmental variables was measured and five samples of the larval insect community were collected across the main channel and off channel habitat. Compositional variation of Trichoptera vs. Odonata was compared using a multivariate test for homogeneity in dispersions, and ordination techniques are used to explore the relative importance of spatial and environmental factors in determining species composition. Results are discussed in the context of biodiversity assessment, with particular emphasis on how taxon specific variation in biodiversity patterns could affect the interpretation of biomonitoring data.