The Upper Murrumbidgee River holds the largest population of the endangered Macquarie Perch (Maccas) in NSW, and one of the largest in Australia. The population has a 95 km long ‘recruitment reach’ with limited public access where regular monitoring demonstrates annual recruitment. The fly in the ointment is the presence of Tantangara Dam, constructed in 1960, approximately 30 km upstream of the top of the recruitment reach. Tantangara dam diverts 90–99% of annual flows to the adjacent Eucumbene catchment as part of the Snowy Hydroelectric Scheme. Abundance of young-of-year Maccas is usually highest towards the upstream end of the recruitment reach, with the consistently high abundance of this age class suggesting that the population was ‘doing ok’. Genetic analysis of finclips collected between 2020 and 2023 tells a different story, with extremely low effective population size, declining genetic diversity, high inbreeding, and low between-site connectivity at upstream end of the reach. Results of the genetic investigations demonstrate that relying on simple measures of recruitment strength can be misleading. Urgent management intervention to improve population connectivity and augment genetic diversity is required to secure the future for this important population. Genetic monitoring will assess whether interventions are working as intended.