Alpine ecosystems are vulnerable to disturbance from habitat loss, climate change, and invasive species. In Australian alpine regions, introduced trout (Salmo trutta and Oncorhynchus mykiss) have been widely established for recreational fishing and may significantly affect native aquatic communities. This study aimed to investigate the influence of trout presence on macroinvertebrate assemblages in alpine streams of the Bogong High Plains, Victoria. It was hypothesized that the presence of trout would negatively impact species diversity, reduce average size class, and alter community composition of macroinvertebrates. Barriers to trout dispersal were used to delineate sites with and without trout, supported by visual surveys and environmental DNA (eDNA). Macroinvertebrates were sampled using kick and drift nets to assess the impacts of trout presence on both drifting and benthic communities. We found that trout presence had a greater impact on the community composition of drifting macroinvertebrates than on benthic assemblages. Drift samples from sites containing trout exhibited greater compositional similarity than those from trout-free sites, indicating that trout presence may lead to homogenisation of drifting communities. Macroinvertebrate size was not significantly affected within benthic communities; however, drift samples from trout-containing sites showed both a reduction in mean body size and a shift in size distributions towards smaller individuals. These patterns suggest that trout predation may selectively reduce the abundance of larger-bodied taxa and influence which species enter the drift, resulting in altered drift community structure without corresponding changes in benthic assemblages. These findings improve our understanding of invasive trout impacts in Australian alpine ecosystems and provide evidence to support management strategies aimed at conserving freshwater biodiversity.