River-floodplains are thought to be hotspots of productivity, yet few studies have quantified their contribution to fueling montane river ecosystems, or the consequences should their connectivity be lost. During summer-fall 2006, we compared availability and retention of basal resources in five reference-condition floodplains to a dredge-mined segment in the Salmon River basin, central Idaho. The dredged segment has a simplified channel and limited riparian vegetation, thus we hypothesized it would support less periphyton, receive fewer allochthonous inputs, and retain less organic matter. We observed that the total biomass of chlorophyll a was actually higher in the dredged versus reference segments, though filamentous forms dominated the dredged segment and production remains to be estimated. Allochthonous input was greatest to reference segments, yet fluxes to the dredged segment were within the range of reference values. In contrast, estimates of potential surface (via leaf-release) and subsurface (via NaCl tracer) organic matter retention indicated reference segments had more than five-fold greater retentive capacity. These measures will be combined with estimates of invertebrate secondary production and abundance of aquatic and terrestrial vertebrates, in an attempt to quantify the importance of intact river-floodplains and the potential for restoration of impaired floodplains in this region.