Riparian revegetation is a standard management tool employed to improve instream habitat, biodiversity, water quality, reduce erosion and achieve thermal buffering. However, the scientific understanding of what it takes to restore these systems is complicated, with financial and organisational limitations to the widespread use of Before-After-Control-Impact (BACI) studies. Where works to remove invasive riparian monocultures of Salix spp. act as a disturbance to stream ecosystems, there can be increased time-lags between management interventions and positive outcomes, making it difficult to predict outcomes with certainty. We had the opportunity to conduct a BACI study of a willow removal and revegetation project along a 3-km reach of the East Barwon River from 2020-2023. We collected four rounds of water quality data, two surveys of instream macrophyte assemblages, and five rounds of channel transect and flow measurements to investigate changes associated with the removal works. Opportunistically, a second Before-After study was also taken at a site where 400 m Salix spp. and Glyceria spp. had been removed upstream. We found a high pulse of high turbidity, nutrients, and E. coli during the willow removal works, changes to some aquatic macrophytes located in the stream, increases to minimum dissolved oxygen levels and diurnal range of dissolved oxygen. We also found increased stream temperatures following the Salix spp. and Glyceria spp. removals. Despite the works studied occurring along very similar streams, the response to invasive species removal varied between the two locations. This was likely due to differences between the main invasive species removed (willows vs. Glyceria spp.), and the differing influence of the West Barwon Reservoir along both reaches. These data provide holistic insight into the early stages of willow removal, Glyceria spp. removal and revegetation in low-order streams, and through partnership with Barwon Water, will hopefully form the foundation for ongoing monitoring.