© 2017 The Authors. Earth Surface Processes and Landforms published by John Wiley & Sons Ltd. Bifurcations are key geomorphological nodes in anabranching and braided fluvial channels, controlling local bed morphology, the routing of sediment and water, and ultimately defining the stability of their associated diffluence–confluence unit. Recently, numerical modelling of bifurcations has focused on the relationship between flow conditions and the partitioning of sediment between the bifurcate channels. Herein, we report on field observations spanning September 2013 to July 2014 of the three-dimensional flow structure, bed morphological change and partitioning of both flow discharge and suspended sediment through a large diffluence–confluence unit on the Mekong River, Cambodia, across a range of flow stages (from 13 500 to 27 000 m 3 s −1 ). Analysis of discharge and sediment load throughout the diffluence–confluence unit reveals that during the highest flows (Q = 27 000 m 3 s −1 ), the downstream island complex is a net sink of sediment (losing 2600 ± 2000 kg s −1 between the diffluence and confluence), whereas during the rising limb (Q = 19 500 m 3 s −1 ) and falling limb flows (Q = 13 500 m 3 s −1 ) the sediment balance is in quasi-equilibrium. We show that the discharge asymmetry of the bifurcation varies with discharge and highlight that the influence of upstream curvature-induced water surface slope and bed morphological change may be first-order controls on bifurcation configuration. Comparison of our field data to existing bifurcation stability diagrams reveals that during lower (rising and falling limb) flow the bifurcation may be classified as unstable, yet transitions to a stable condition at high flows. However, over the long term (1959–2013) aerial imagery reveals the diffluence–confluence unit to be fairly stable. We propose, therefore, that the long-term stability of the bifurcation, as well as the larger channel planform and morphology of the diffluence–confluence unit, may be controlled by the dominant sediment transport regime of the system. © 2017 The Authors. Earth Surface Processes and Landforms published by John Wiley & Sons Ltd.