Stocking of native fishes is conducted to augment riverine fisheries in many parts of the world, yet most stocking activities are conducted without empirical information on their effectiveness or impacts. In the Murray–Darling Basin (MDB), Australia, stocking has been underway for several decades to maintain recreational fisheries. We stocked chemically tagged golden perch (Macquaria ambigua) fingerlings in three rivers to determine the proportions of stocked fish within populations of the species. Stocked sites were monitored for up to 5 years in the Murrumbidgee River, Edward River and Billabong Creek and non-stocked sites were monitored in the Murray River. Catch per unit effort of stocked year classes increased substantially in Billabong Creek, with stocked fish contributing 100 (2005), 79 (2006) and 92% (2007). Chemically tagged fish comprised 18–38% of the respective age classes in the Murrumbidgee and Edward rivers and there was little evidence of natural recruitment in the non-stocked Murray River. Tagged fish generally attained the legal minimum size within 4 years and had dispersed up to 60 km from the original release location. Our results demonstrate that artificial stocking has the potential to strongly influence the abundance and population structure of golden perch in rivers of the MDB.