With climate change, Victoria’s rivers are predicted to become drier but also face more intense and frequent floods. In October 2022, much of northern Victoria experienced record high river flows and flood levels. Although floods support important ecosystem functions, they are also associated with erosion, mass breeding events of exotic species, and hypoxic blackwater. The impacts of floods are often highly visible. However, studies of ecological recovery in the months and years after an event are much less common. We drew on existing monitoring projects in most major rivers in northern Victoria to examine recovery pathways for fish species following the 2022 floods. As widely observed, native fish numbers declined, and invasive fish numbers increased in the 6 months following floods. After 18 months, native fish abundance remained low but exhibited early signs of recovery, particularly in species able to move long distances. Notably, abundances of the invasive carp had begun to decrease 18 months after floods but those of European Perch had increased. Relatively slow recovery suggests that native fish species may be susceptible to future disturbances (e.g., droughts or more floods) and highlights a potential need for management interventions to bolster native fish populations and control introduced species.