1. Water extraction from arid-zone rivers increases the time between floods across their floodplain wetlands. Less frequent flooding in Australian arid-zone rivers has impaired waterbird and fish breeding, killed riparian vegetation and diminished invertebrate and macrophyte communities. Restoration currently focuses on reinstating floods to rejuvenate floodplain wetlands, yet indicators to measure the success of this are poorly developed. 2. We explored the application of criteria for ecologically successful river restoration to potential restoration of floodplain wetlands on the Darling River, arid-zone Australia. Using emergence of micro-invertebrates from resting eggs as an indicator, we compared responses of taxa richness, densities and community composition in floodplain lakes with different inundation histories. 3. Increased drying of floodplain lakes reduced the number of micro-invertebrate taxa. Several key taxa were absent and faunal densities (particularly cladocerans) were reduced when the duration of drying increased from 6 to 20 years. 4. A conceptual model of the ecological mechanisms by which restoration of flooding regime could achieve the target of preserving micro-invertebrate community resilience predicts that reducing the dry period between floods will minimize losses of viable resting eggs. Protection of this 'egg bank' permits a boom in micro-invertebrates after flooding, promoting successful recruitment by native fish and waterbirds. 5. Synthesis and applications. In arid-zone rivers, micro-invertebrate densities and community composition are useful indicators of the impact of reduced flooding as a result of water extraction. Critical to successful native fish recruitment as their first feed and as prey for waterbirds, micro-invertebrates are a potential early indicator of responses by higher trophic levels. Taxon richness, density and key taxa present after flooding, all indicators of resilience, can be incorporated into targets for arid-zone river restoration. For example, one restoration target may be microcrustacean densities between 100 and 1000 L⁻¹ within 2–3 weeks after spring flooding. These criteria can be applied to measure the ecological success of restoration projects seeking to recover natural flood regimes. Given the high economic cost of water in arid zones, convincing demonstrations of the ecological success of environmental water allocations are crucial.