Bed material transport at river bifurcations is crucial for channel stability and downstream geomorphic dynamics. However, measurements of bed material transport at bifurcations of large alluvial rivers are difficult to make, and standard estimates based on the assumption of proportional partitioning of flow and bedload transport at bifurcations may be erroneous. In this study, we employed a combined approach based on observed topographic change (erosion/deposition) and bed material transport predicted from a one‐dimensional model to investigate bed material fluxes near the engineering‐controlled Mississippi‐Atchafalaya River diversion, which is of great importance to sediment distribution and delivery to Louisiana's coast. Yang's (1973) sediment transport equation was utilized to estimate daily bed material loads upstream, downstream, and through the diversion during 2004–2013. Bathymetric changes in these channels were assessed with single beam data collected in 2004 and 2013. Results show that over the study period, 24% of the Mississippi River flow was diverted into the Atchafalaya River, while the rest remained in the mainstem Mississippi. Upstream of the diversion, the bed material yield was predicted to be 201 million metric tons (MT), of which approximately 35 MT (i.e., 17%) passed through the bifurcation channel to the Atchafalaya River. The findings from this study reveal that in the mainstem Mississippi, the percentage of bed material diversion (83%) is larger than the percentage of flow diversion (76%); Conversely, the diversion channel receives a disproportionate amount of flow (24%) relative to bed material supply (17%). Consequently, severe bed scouring occurred in the controlled Outflow Channel to the Atchafalaya River, while riverbed aggradation progressed in the mainstem Mississippi downstream of the diversion structures, implying reduced flow capacity and potential risk of a high backwater during megafloods. The study demonstrates that Yang's sediment transport equation provides plausible results of bed material fluxes for a highly complicated large river diversion, and that integration of the sediment transport equation with observed morphological changes in riverbed is a valuable approach to investigate sediment dynamics at controlled river bifurcations.