We present a quantitative analysis of habitat availability in a highly regulated lowland river, comparing a restored reach with two reference reaches: an un-restored, channelized reach, and a least-altered reach. We evaluate the effects of channel modifications in terms of distributions of depth and velocity as well as distributions and availability of habitats thought to be supportive of an endangered fish, the pallid sturgeon (Scaphirhynchus albus). It has been hypothesized that hydraulic conditions that support food production and foraging may limit growth and survival of juvenile pallid sturgeon. To evaluate conditions that support these habitats, we constructed two-dimensional hydrodynamic models for the three study reaches, two located in the Lower Missouri River (channelized and restored reaches) and one in the Yellowstone River (least-altered reach). Comparability among the reaches was improved by scaling by bankfull discharge and bankfull channel area. The analysis shows that construction of side-channel chutes and increased floodplain connectivity increase the availability of foraging habitat, resulting in a system that is more similar to the reference reach on the Yellowstone River. The availability of food-producing habitat is low in all reaches at flows less than bankfull, but the two reaches in the Lower Missouri River – channelized and restored – display a threshold-like response as flows overtop channel banks, reflecting the persistent effects of channelization on hydraulics in the main channel. These high lateral gradients result in punctuated ecological events corresponding to flows in excess of bankfull discharge. This threshold effect in the restored reach remains distinct from that of the least-altered reference reach, where hydraulic changes are less abrupt and overbank flows more gradually inundate the adjacent floodplain. The habitat curves observed in the reference reach on the Yellowstone River may not be attainable within the channelized system on the Missouri River, but the documented hydraulic patterns can be used to inform ongoing channel modifications. Although scaling to bankfull dimensions and discharges provides a basis for comparing the three reaches, implementation of the reference reach concept was complicated by differences in flow-frequency distributions among sites. In particular, habitat availability in the least-altered Yellowstone River reach is affected by increased frequency of low-flow events (less than 0.5 times bankfull flow) and moderately high-flow events (greater than 1.5 times bankfull flow) compared to downstream reaches on the Lower Missouri River.