Large-scale desalination is used increasingly to address growing freshwater demands and climate uncertainty. Discharge of hypersaline brine from desalination operations has the potential to impact marine ecosystems. Here, we used a seven-year Multiple-Before-After-Control-Impact experiment to test the hypothesis that hypersaline discharge from reverse-osmosis desalination alters temperate reef communities. Using replicated, video-based surveys at eight sites, we sampled fish, invertebrate and algal assemblages before, during and after the discharge of hypersaline brine. Following the commencement of discharging, there was a 279% increase in the abundance of fish around the outlet, although some sessile invertebrates were negatively impacted. The construction of the desalination outlet and subsequent discharge caused a decrease in the cover of Ecklonia radiata (kelp) and an increase in the cover of algal turfs. Overall, we found the influence of hypersaline discharge on temperate reef biota to be spatially localized, with the area around the outlet continuing to support rich and diverse faunal communities. In some cases, therefore, the marine environmental consequences of large-scale, well designed, desalination operations may be appropriately balanced against the positive benefits of improved water security.