In canyon rivers, debris fan constrictions create rapids and downstream pools characterized by secondary flow structures that are closely linked to channel morphology. In this paper we describe detailed measurements of the three‐dimensional flow structure and sandbar dynamics of two pools along the Colorado River in the Grand Canyon during a controlled flood release from Glen Canyon Dam. Results indicate that the pools are characterized by large lateral recirculation zones (eddies) resulting from flow separation downstream from the channel constrictions, as well as helical flow structures in the main channel and eddy. The lateral recirculation zones are low‐velocity areas conducive to fine sediment deposition, particularly in the vicinity of the separation and reattachment points and are thus the dominant flow structures controlling sandbar dynamics. The helical flow structures also affect morphology but appear secondary in importance to the lateral eddies. During the controlled flood, sandbars in the separation and reattachment zones at both sites tended to build gradually during the rising limb and peak flow. Deposition in shallow water on the sandbars was accompanied by erosion in deeper water along the sandbar slope at the interface with the main channel. Erosion occurred via rapid mass failures as well as by gradual boundary shear stress driven processes. The flow structures and morphologic links at our study sites are similar to those identified in other river environments, in particular sharply curved meanders and channel confluences where the coexistence of lateral recirculation and helical flows has been documented.