Didymosphenia geminata is a bloom-forming diatom that has invaded numerous temperate rivers globally. Proliferations of D. geminata can result in negative effects on invaded communities. Ecological theory suggests impacts may vary associated with trait variation in both invaded communities and the invader. Trait commonalities related to organism size are rarely considered, yet are expected to influence the outcomes of ecological (niche and neutral) processes and invader effects. We hypothesised that D. geminata would impact diversity and community composition, with effects varying between size classes, influenced by niche and spatial gradients. To examine this hypothesis, we surveyed 55 rivers along a gradient of D. geminata biomass in the South Island, New Zealand, collecting data on algal and invertebrate communities, 33 spatial predictors, and 111 physical and chemical predictors. Didymosphenia geminata biomass was associated with increased species richness in both algal and invertebrate assemblages, but blooms reduced beta-diversity resulting in more homogenous communities. Both niche and neutral processes influenced community assembly and invader effects, which varied between algae and invertebrates. However, D. geminata appeared to have a dominant influence on both communities, irrespective of organism size. These findings reinforce the substantial negative effect invasive species such as D. geminata can cause in invaded ecosystems.