1. Floodplain wetlands are productive components of lowland rivers and are thought to be important habitat and nurseries for many fish species. Fish assemblages inhabiting floodplain wetlands vary considerably through space and time and are largely shaped by wetting ⁄drying cycles, although there is little understanding how many aspects of flooding (e.g. magnitude, timing, duration, frequency) influence the fish assemblages. As a consequence, decisions on flooding of wetlands by managers aimed at restoring native fish assemblages are often based on limited knowledge. 2. This study examined the importance of total duration of flooding on the temporal and spatial dynamics of wetland fish assemblages in the Murray River, in south-eastern Australia. The study examined: (i) how the abundance of 0+ and 1+ fish varied with wetland, season and the duration of wetland filling; (ii) how environmental parameters, including food production changed in relation to the duration of wetland filling; (iii) changes in condition indices for the most abundant species and (iv) changes in species richness and total abundance over time. 3. The 0+ fish assemblage varied more through space and time than the 1+ assemblage. Longer cumulative river–wetland filling was associated with greater total abundances of newly recruited (0+) fish; this was particularly true for common carp (Cyprinus carpio, alien) and carp gudgeon (Hypseleotris spp., native). The body condition of carp gudgeon also increased with the duration of filling, even though static measures of food production declined. The small flooding events that occurred as part of this study did not translate into measurable improvements in the fish assemblage over the longer term (3 years), but did prevent wetlands from drying and thus maintained these habitats as refuges.