Invasions by non-indigenous organisms are a significant global threat to biodiversity and the structure and function of ecosystems. However, the effects of invasive species on biodiversity and community structure can be difficult to predict. In part this is due to fundamental trait differences among invaded assemblages and invaders, causing the strength of ecological processes to vary (e.g. niche filtering and neutral dynamics). Didymosphenia geminata is considered an invasive freshwater diatom in New Zealand, and its impacts are of major concern in temperate rivers and streams globally. D. geminata alters primary productivity and modifies benthic habitats, exerting effects on numerous components of aquatic ecosystems. We examined D. geminata influences on algal and macroinvertebrate communities by assessing the dual importance niche and neutral processes (represented by distance decay). We hypothesised that D. geminata would be a strong ecological determinant within both invertebrate and algal communities, but that differences in traits related to organism size would be reflected in variation in the relative strengths of niche and neutral processes. To test hypotheses, we surveyed 55 sites across a gradient of D. geminata biomass examining two community datasets and 111 physicochemical and 33 spatial predictors. We found D. geminata biomass was associated with greater species richness in algal and invertebrate assemblages, but reduced beta diversity driven by losses of rare taxa, homogenising assemblages. While D. geminata biomass strongly influenced both assemblages, variance partitioning showed abiotic niche filters and spatial gradients became increasingly important with increasing organism size. Our results reinforce variation in ecological responses related to size should be accounted for when considering the impacts of an invasive species like D. geminata, and such variance is putatively important within ecology. D. geminata has impacts disproportionate to competing niche filters with effects suggesting D. geminata may be considered an ecosystem engineer.