The Gunbower and Koondrook-Perricoota Forest (KPF) includes a natural floodplain wetland system that has suffered for many years from a lack of water as a result of water extraction practices in the Murray River. The site was targeted with a combination of environmental water allocations and environmental works programs to manage the distribution and retention of water and ultimately improve its ecological health. A major ecological objective for the Gunbower Koondrook-Perricoota Forest is ‘healthy populations of resident native fish in wetlands’. Golden perch, a large-bodied native species utilise similar habitat on the floodplain proper and floodplain channels between nearby Cobram and Yarrawonga and were documented utilising drying waterholes in the vicinity of the nearby Murrumbidgee River as far back as 1917. We report on an acoustic monitoring survey in 2016 when during a natural flood, none of 14 tagged Golden Perch tagged in the adjacent main river channel entered the forest. Yet at the same time, 34 of 44 tagged Common carp moved into the forest when passage became available from rising waters. Further, seven years of consecutive autumn condition monitoring on the KPF floodplain has failed to sample a single golden perch young-of-year in KPF, and only two adults have been sampled within KPF during that time. In addition, intensive electrofishing and fyke netting of the inlet channel during the first managed event in 2014 failed to collect any golden perch, and none were trapped in the fishways. We suggest that it is important that golden perch and other native large-bodied fish continue to be considered when operating the regulators during future events, including monitoring of fish accumulations at the outlet regulator and fishway trapping.