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The spatial patterns of transport‐effective flows at confluences and the relation of these patterns to channel morphology remain poorly understood. This field study uses acoustic Doppler current profiler measurements to explore the spatial structure of different transport‐effective flows at three small stream confluences where measurements of flow structure have been obtained previously using electromagnetic current meters or acoustic Doppler velocimeters for events incapable of mobilizing bed material or for transport‐effective events with much smaller discharges. Results show that flow accelerates from upstream to downstream for all six measured flows and that in each case a distinct region of velocity deficit exists within the confluence. Accelerating flow within this velocity‐deficit region eventually transforms into the high‐velocity core of flow downstream of the confluence. Patterns of secondary flow are indicative of helical motion, with some helical cells exhibiting senses of rotation inconsistent with patterns of streamline curvature defined by patterns of depth‐averaged velocity vectors—a type of fluid motion that contrasts with flow structure documented at lower stages. Channel form, especially bed morphology, generally reflects acceleration of flow at the confluences; all three sites exhibit zones of scour. Despite mobility of bed material during measured flows, channel morphology does not change substantially at any of the sites, but systematic change in channel form for two different transport‐effective events with different momentum flux ratios is observed at one of the three confluences. At this confluence, the type of change documented during the two events is consistent with previous work on changes in morphology before and after events with different momentum flux ratios. The results of this study improve understanding of the connections between flow structure and channel form at small lowland stream confluences.