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INTRODUCTION Substrate composition affects primary and secondary production in riverine ecosystems. Periphyton and invertebrates, the food base of the fish community, depend on rock surfaces for attachment sites; in addition, invertebrates depend on the interstitial voids among rocks for shelter and feeding sites. Because the transport, sorting and deposition of coarse and fine-grained sediments is largely determined by the flow regime, gaining a better understanding of the link between streamflow, substrate characteristics, and food availability will allow managers to more effectively manipulate flows to maintain and enhance native fish habitat. Periodic mobilization of coarse bed material is needed to winnow fine sediments, primarily silt and sand, from the gravels and cobbles (Kondolf and Wilcock 1996). Without periodic bed mobilization, deposited fines eventually clog interstitial voids among rocks leaving fewer and fewer sheltered sites within which invertebrates can live. In habitats other than riffles, even the top surfaces of rocks may become covered with fines leaving little area for algal attachment. Determining what flows are necessary to mobilize the bed addresses two important issues related to management of spring flows: magnitude and duration, i.e., what volume of water is needed to move rocks in an instant in time and what period of time is required for this volume of water to adequately flush fines from the bed: What is not addressed is the issue of frequency, i.e., how often the bed must be mobilized and flushed of fines to maintain maximum productivity within the benthos. The answer to this third question depends on the rate of deposition of fines within voids in the intervening periods between flushing flows. We have initiated a monitoring program designed to measure the rate of deposition of fine sediments within cobble substrates in run and riffle habitats in the upper Colorado River. The measurement used for monitoring is total `depth-to-embeddedness' (total DTE) which is the distance from the top of the rocks on the bed surface down to the top of the layer of fines in which the cobbles are embedded (Fig. 1). This distance or depth provides a standard measure of available space for benthic biota to live. Substrate particle size is also measured so that the depth measurement can be used to estimate the number of free rocks (relative DTE) making up the layer above the level of embeddedness. The process makes two assumptions: 1) in the absence of other limitations, surficial space limits algal and macroinvertebrate production, and 2) that surfaces and voids above the layer of fines is available for macroinvertebrate use and that an increase in depth to embeddedness therefore allows for greater productivity of benthic biota. The monitoring process consists of measuring depth-to-embeddedness at consistent locations during the runoff and base-flow periods and is continued over a period of years of varying flow regimes. To detect trends, several years will likely be required. We here describe the monitoring protocol and report the results from the first two years of the program.