Migration for spawning or dispersal is common among freshwater fishes. Migration is often integrally linked to environmental factors such as water temperature and flow regime. Water infrastructure such as dams and weirs can alter flows and impact migration opportunities for many species. We used acoustic telemetry and flow records to inform migratory movements and barrier passage for two iconic fish species of the Murray-Darling Basin (MDB): golden perch (Macquaria ambigua) and Murray cod (Maccullochella peelii). Over a four year period we tagged 264 golden perch and 40 Murray cod, and tracked their movements using 62 acoustic receivers installed along 850 km of the Condamine-Balonne Rivers in the Queensland MDB. Between May 2018 and July 2022 over 11.9 million detections had been recorded on the array. A total of 22% of golden perch and 65% of Murray cod migrated from their ‘home pool’ in both upstream and downstream directions. Analyses revealed the maximum distance moved on any one flow event for golden perch was 68 km and for Murray cod 80 km. The average movement distance for golden perch was 3.52 km and for Murray cod was 3.21 km. The mean daily flow for golden perch movement was 34.92 m3s-1 and for Murray cod was 39.82 m3s-1. Golden perch movements were more frequent between October and May, coinciding with increased river discharge. Murray cod movements, however, were equally likely throughout the year. Although the weirs within the study area ‘drowned out’ on some flows, theoretically enabling unhindered fish passage, only a small number of individuals passed the weirs. Our approach of using a long-term movement study, across extensive river reaches has provided detailed life history flow information and highlighted the impact of instream barriers for these species. The outcomes of this project will inform water planning in the Queensland MDB.