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Background The size of the bed material controls the amount and type of habitat for invertebrates. If the bed is composed solely of fine materials (< 2 mm), the spaces between particles are too small for most organisms. Coarser materials provide a variety of niches important for benthic invertebrates, as well as some small fish. Larger particles also allow more interflow through the bed, increasing substrate permeability and dissolved oxygen concentrations. Even small declines in intergravel dissolved oxygen can affect the survival of invertebrates as well as some fish eggs (MacDonald et al. 1991). The physical effects of embeddedness are similar to the effects of a decrease in bed material particle size. Biologically, areas with high embeddedness have very little space for invertebrates or juvenile fish to hide or seek protection from the current. The filling in of spaces among larger particles reduces interstitial habitat. Similarly, attachment area for periphyton is limited with the reduction in surface area associated with increased embeddedness (MacDonald et al. 1991). Deposition of fine materials without frequent flushing may be self-perpetuating. In some cases the onset of bedload transport is delayed, i.e., the bed is more resistant to mobilization, when the interstitial spaces are filled with fine sediment (Reid et al. 1985, Chapman and McLeod 1987). The result is a decreased frequency of bedload transport which in turn provides more time for further deposition of fines and fewer opportunities for fines to be winnowed from the substrate during high flows (Beschta and Jackson 1979). Gravel river beds are typically composed of surface and subsurface layers. The surface layer, sometimes called a pavement or mobile armour, is coarser than the subsurface material. Milhous (1973) found that the role of the mobile armour on the deposition and retention of fines is quite important. At low flows, the immobile surface layer acts as a sink for suspended sediment, which deposits in the interface between the pavement bottom and the subsurface top. This zone acts as a silt reservoir: at high discharge when the pavement is set in motion, the bed becomes a source of suspended sediment as fines are winnowed out. O'Brien (1987), studying the Yampa River, observed that in the absence of gravel mobilization fines could be cleaned from the bed to a depth below the bed surface equal to the median grain size of the surface layer. Both Milhous (1973), O'Brien (1987) and Wilcock et al. (1996) have emphasized the necessity of surface layer mobilization for removing fines below the surface layer. Most North American studies involving effects of sedimentation on stream communities have been conducted either in the Pacific Northwest or in the northeastern United States where problems associated with increased sedimentation have resulted from forest harvesting, road construction, and farming (Clarke and Scruton 1997). Researchers have successfully linked sediment increases to reduced survival of age-O salmonids during emergence (Platts et al. 1989, Scrivener and Brownlee 1989) and changes in the abundance and structure of benthic macroinvertebrate communities (Lenat et al. 1981). Comparatively little such work has been done in the upper Colorado River where the endangered Colorado squawfish (Ptychocheilus 3