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INTRODUCTION A usual consequence of river regulation by main stem dams is reduction of native species diversity (Holden 1979, Ward and Stanford 1979, Stanford et al. 1996). Such reductions typically result from loss of habitat, blocked migration routes, or alteration of natural ecosystem attributes and functioning. For example, in streams of the western USA, dams reduce springtime discharge maxima from snow melt so that main-channel and floodplain interaction is reduced or eliminated. Deep-releases from reservoirs reduce spring and summer water temperature of streams downstream of dams and cause shifts in composition offish and invertebrate communities from warm stenothennic native species to non-indigenous cold-tolerant eurytherms. Remnant populations of native fishes may persist as adults in highly regulated reaches if they are long-lived and have high dispersal capability, but reproduction is often reduced or eliminated by cold spring and summer water temperatures. Non-indigenous species, which are often supported by dam-created habitat or a reservoir source population, are another mechanism for reduction of native species. Such reductions may manifest through negative effects of predation, competition, or introduction of diseases and parasites. Effects of introduced fishes maybe especially problematic in western USA river systems because indigenous communities have naturally low diversity and may be prone to invasion (Minckley and Deacon 1968, Stanford and Ward 1-986, Moyle et al. 1986, Carlson and Muth 1989, Minckley and Deacon 1991). A protocol for restoration of regulated rivers (Stanford et al. 1996) that was derived from principles of lotic ecology calls for re-establishment of intra- and inter-annual habitat linkages along lateral, vertical, and longitudinal stream axes by restoring more natural flow, sediment, and temperature regimes (Ward 1989, Petts 1984, Ward and Stanford 1995, Poff et al. 1997). Examples of key processes that may facilitate recovery of biota are re-establishment of annual flow maxima to maintain channel geomorphology and flood plain connectedness, reduction of baseflow fluctuations to enhance stability and food web functioning of low velocity nearshore