Abstract. Understanding the spatial organization of river systems in light of natural and anthropogenic change is extremely important because it can provide information to assess, manage, and restore them to ameliorate worldwide freshwater fauna declines. For gravel- and cobble-bedded alluvial rivers studies spanning analytical, empirical and numerical domains suggest that at channel-forming flows there is a tendency towards covarying bankfull bed and width undulations amongst morphologic units such as pools and riffles, whereby relatively wide areas have relatively higher minimum bed elevations and relatively narrow areas have relatively lower minimum bed elevations. The goal of this study was to determine whether minimum bed elevation and flow-dependent channel top width are organized in a partially confined, incising gravel–cobbled bed river with multiple spatial scales of anthropogenic and natural landform heterogeneity across a range of discharges. A key result is that the test river exhibited covarying oscillations of minimum bed elevation and channel top width across all flows analyzed. These covarying oscillations were found to be quasiperiodic at channel-forming flows, scaling with the length scales of bars, pools and riffles. Thus, it appears that alluvial rivers organize their topography to have quasiperiodic, shallow and wide or narrow and deep cross section geometry, even despite ongoing, centennial-scale incision. Presumably these covarying oscillations are linked to hydrogeomorphic mechanisms associated with alluvial river channel maintenance. The biggest conclusion from this study is that alluvial rivers are defined more so by variability in topography and flow than mean conditions. Broader impacts of this study are that the methods provide a framework for characterizing longitudinal and flow-dependent variability in rivers for assessing geomorphic structure and aquatic habitat in space, and if repeated, through time.