Large catchment basins may be viewed as ecosystems in which natural and cultural attributes interact. Contemporary river ecology emphasizes the four-dimensional nature of the river continuum and the propensity for riverine biodiversity and bioproduction to be largely controlled by habitat maintenance processes, such as cut and fill alluviation mediated by catchment water yield. Stream regulation reduces annual flow amplitude, increases baseflow variation and changes temperature, mass transport and other important biophysical patterns and attributes. As a result, ecological connectivity between upstream and downstream reaches and between channels, ground waters and floodplains may be severed. Native biodiversity and bioproduction usually are reduced or changed and non-native biota proliferate. Regulated rivers regain normative attributes as distance from the dam increases and in relation to the mode of dam operation. Therefore, dam operations can be used to restructure altered temperature and flow regimes which, coupled with pollution abatement and management of non-native biota, enables natural processes to restore damaged habitats along the river's course. The expectation is recovery of depressed populations of native species. The protocol requires: restoring peak flows needed to reconnect and periodically reconfigure channel and floodplain habitats; stabilizing baseflows to revitalize food-webs in shallow water habitats; reconstituting seasonal temperature patterns (e.g. by construction of depth selective withdrawal systems on storage dams); maximizing dam passage to allow recovery of fish metapopulation structure; instituting a management belief system that relies upon natural habitat restoration and maintenance, as opposed to artificial propagation, installation of artificial instream structures (river engineering) and predator control; and, practising adaptive ecosystem management. Our restoration protocol should be viewed as an hypothesis derived from the principles of river ecology. Although restoration to aboriginal state is not expected, nor necessarily desired, recovering some large portion of the lost capacity to sustain native biodiversity and bioproduction is possible by management for processes that maintain normative habitat conditions. The cost may be less than expected because the river can do most of the work.