The role that natural instream barriers take in shaping riverine fish communities is frequently overlooked, with the focus most often on man-made structures such as dams and weirs. There have been few detailed studies of fish communities in the coastal rivers of south-eastern Australia. The Clarence Basin is located in northern New South Wales (NSW) and is one of the largest of these coastal drainages, encompassing an area in excess of 20,000 km2. The system is largely unregulated and plays an important role in the recreational and commercial fisheries of NSW. The aim of this study was to better understand the relationships among river discharge, instream barriers and fish ecology across the freshwater and estuarine reaches of the Clarence Basin. Electrofishing surveys and acoustic telemetry were used to determine the effect of four potential fish passage barriers in the Clarence Basin 2006-2017. Based on bi-annual electrofishing surveys, the natural barrier created by the Clarence Gorge had the greatest effect on the fish assemblages in the system. Acoustic telemetry was used to study the movement patterns of five large-bodied fish species native to the system; three migratory and two non-migratory. Large-scale linear movements were undertaken by all three migratory species, facilitated by increases in river discharge. Longer linear movements from the freshwater reaches to the estuary aligned with individual species breeding season and were often impeded by natural and anthropogenic barriers alike. In comparison, the two non-migratory species moved relatively short distances and mainly during late-winter and spring for breeding. The current study has provided an insight into the role river discharge and barriers have in shaping the structure of fish assemblages in coastal river systems. These results highlight the challenges faced by natural resource managers as climate change and anthropogenic influences place ever increasing pressure on coastal ecosystems.