Abstract Many fish rely on being able to move between rivers and floodplains to fulfil key life history events, but river regulation has reduced floodplain inundation compromising these connections and causing the loss of ecosystem function more generally. Managed inundations are being trialled in some systems as a solution, whereby engineered floods using built infrastructure, such as floodplain regulators, are used to deliver water to inundate floodplains. However, the use of managed inundations is still in early stages and their outcomes for native fish have been rarely assessed. We present the results from a series of investigations assessing the effectiveness of two managed inundations on the native fish community in a large floodplain in south‐eastern Australia. We firstly described changes in fish assemblages in wetlands before and after managed inundation (Aim 1). We then examined which potential exits are used by golden perch, a highly mobile species that regularly moves between rivers and floodplains (Aim 2), and then assessed outmigration patterns of native and non‐native species during receding phase from one of the major golden perch exits via a fishlock (Aim 3). Finally, we conducted two experiments to test if it was possible to modify operation of the fishlock to maximise fish movement by varying the length of the operating cycle, or whether operation occurs during the day or night (Aim 4). We found that native fish dominated the catch in wetlands before drawdown of the managed inundation, but that non‐native species, especially young‐of‐year carp, dominated after the drawdown (Aim 1). Outmigrating golden perch left the floodplain wetlands in a variety of locations but predominantly through a fishlock, which is a type of fishway (Aim 2). At this fishlock, native fish outmigrated before and during the early phase of the floodplain recession, moving to permanent riverine habitats, whereas non‐native fish (mostly carp) tended to migrate later in the recession especially as water levels dropped (Aim 3). There were no substantive differences in the numbers and size of fish moving through the fishlock at different operating cycle times (Aim 4). While there were no differences in numbers of non‐native carp migrating during the day or night, native species (carp gudgeon and Australian smelt) were more common during the day. Our study has provided knowledge of the eco‐hydraulic mechanisms of fish movement, in relation to managed inundaitons. This knowledge can be applied to help water managers plan floodplain watering regimes in the Murray‐Darling Basin to benefit native fish, while potentially restricting movement of undesirable non‐native species such as carp. More broadly, our results improve current understanding of fish movement in relation to managed floodplain recession, which is critical given the increased use of such managed inundations, and the need for information to help design and evaluate them.