Removal of invasive macrophytes is a priority for managers, but the ecological effects of removing invasive macrophytes on macroinvertebrate fauna are often unknown. This study investigated the aquatic macroinvertebrate fauna inhabiting the invasive waterfern (Ceratopteris thalictroides) and the effects of waterfern removal on the macroinvertebrate assemblage at Millstream, in the Pilbara, Western Australia. Macroinvertebrates were sampled at unweeded waterfern-dominated reaches, reaches dominated by native macrophytes, and at weeded reaches, 2 weeks, 6 weeks and 3 months post-weeding. Unweeded waterfern harboured a diverse macroinvertebrate assemblage, including nymphs of the short-range endemic damselfly Nososticta pilbara. Macroinvertebrate assemblages differed between waterfern and native macrophytes. At weeded reaches, taxa richness was lowest at 2 weeks post-weeding but increased with time. Macroinvertebrate assemblages at weeded reaches became more like native-dominated reaches as plants regrew. Frequently weeded reaches supported taxa that were rare or absent from waterfern-dominated reaches, particularly suspension-feeders, which were very common at native-dominated reaches. However, odonate assemblages did not recover following weeding. Overall, C. thalictroides did not have profoundly negative impacts on macroinvertebrate biodiversity, and provided suitable habitat to a high diversity of macroinvertebrates including rare Odonata. Although weeding had a negative impact on some taxa, it may also increase habitat patchiness in the Millstream channels, thereby allowing a greater overall diversity of organisms to co-exist.