Dammed rivers are subject to changes in their flow, water-quality, and sediment regimes. Each of these changes may contribute to diminished aquatic habitat quality and quantity. Of the three factors, an altered sediment regime is a particularly unyielding challenge on many dammed rivers. The magnitude of the challenge is illustrated on the Lower Missouri River, where the largest water storage system in North America has decreased the downriver suspended-sediment load to 0.2%–17% of pre-dam loads. In response to the altered sediment regime, the Lower Missouri River channel has incised as much as 3.5 m just downstream of Gavins Point Dam, although the bed has been stable to slightly aggrading at other locations farther downstream. Effects of channel engineering and commercial dredging are superimposed on the broad-scale adjustments to the altered sediment regime.

The altered sediment regime and geomorphic adjustments constrain restoration and management opportunities. Incision and aggradation limit some objectives of flow-regime management: In incising river segments, ecologically desirable reconnection of the floodplain requires discharges that are beyond operational limits, whereas in aggrading river segments, small spring pulses may inundate or saturate low-lying farmlands. Lack of sediment in the incising river segment downstream of Gavins Point Dam also limits sustainable restoration of sand-bar habitat for bird species listed under the Endangered Species Act. Creation of new shallow-water habitat for native fishes involves taking sediment out of floodplain storage and reintroducing most or all of it to the river, raising concerns about increased sediment, nutrient, and contaminant loads. Calculations indicate that effects of individual restoration projects are small relative to background loads, but cumulative effects may depend on sequence and locations of projects. An understanding of current and historical sediment fluxes, and how they vary along the river, provides a quantitative basis for defining management constraints and identifying opportunities.