The Murray-Darling Basin (MDB) covers an area of over 1 million km2 and is subject to the Basin Plan which provides additional water and flow management for environmental purposes. Many MDB native fishes have suffered severe declines in abundance and there is an immediate need for current knowledge to inform both annual and longer-term watering plans. Flow management needs to occur at spatial scales that are most appropriate to the species of concern. This varies from local, site-based applications for species such as Southern pygmy perch to larger landscape (almost the whole basin) scales for Golden perch, which are widespread and highly migratory. These issues have been explored through the development of population models that can predict population outcomes for rehabilitative management actions. Southern Pygmy perch now consists of fragmented localised populations that are dependent on habitat and the absence of alien carp and redfin to survive. Key management actions are the protection of existing and the establishment of additional populations. The population model for management of golden perch incorporates recent research results including movements and recruitment and nursery sites. This species potentially needs to be managed at the landscape scale, covering most of the MDB; provision of connectivity is vital; high flows can enhance recruitment; smaller pulses promote colonization by juveniles; and efforts should be made to provide access and connectivity to key wetland nursery areas for recruitment pulses (such as Menindee lakes). More details on model outputs are provided in the accompanying Todd et al. presentation.