Habitat alteration and destruction are a primary driver of biodiversity loss. There is a plethora of research documenting similarly strong patterns of decline across ecosystem types and spatial scales. However, evolutionary dimensions remain largely unexplored in many systems. For example, little is known about how habitat alteration/loss can lead to phylogenetic deconstruction of ecological assemblages at the local level. That is, while species loss is evident, are some lineages favored over others? Using a long-term dataset of a globally, ecologically important guild of invertebrate consumers, stream leaf “shredders,” we created a phylogenetic tree of the taxa in the regional species pool, calculated mean phylogenetic distinctiveness for > 1000 communities spanning > 10 y period, and related species richness, phylogenetic diversity and distinctiveness to watershed-scale impervious cover. Using a combination of changepoint and compositional analyses, we learned that increasing impervious cover produced marked reductions in all three measures of diversity, and in particular, aid in understanding both phylogenetic diversity and average assemblage phylogenetic distinctiveness. Our findings suggest that, not only are species lost when there is an increase in watershed urbanization, as other studies have demonstrated, but that those lost are members of more distinct lineages relative to the community as a whole.