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The modern Mississippi River (M.R.) Delta is plumbed by the Mississippi and Atchafalaya rivers, setting water and sediment dispersal pathways for Earth's fifth‐largest river system. The Atchafalaya River's (A.R.) partial annexation of discharge from the M.R., particularly between 1926 and 1950, prompted warnings of a rapid river avulsion and the construction of the Old River Control Structure to regulate flow. Natural and anthropogenic causes of this discharge annexation are difficult to disentangle. Here, we develop and validate a hydrodynamic model of flow partitioning through the historic channel network. We then isolate how several key changes to the system affected discharge partitioning and stage at the A.R.‐M.R. diversion. Simulations show that erosion of the upper A.R. can account for 73% of the water discharge increase. Dredging in the lower A.R. between 1932 and 1950 can account for 35% of the water discharge increase, and was also an important control on shear stress distribution. The lower M.R. was slightly erosional during this period, and therefore hindered the A.R. discharge increase. Significant lacustrine delta deposition in A.R. had little effect on partitioning. These findings highlight the importance of A.R. enlargement processes on avulsion dynamics at this site. Given the essential nature of this river junction to the society, transportation, and commerce of the United States, improved attribution of discharge increases may lead to future management strategies that are broadly impactful. Key Points: The rapid increase in discharge to the Atchafalaya River between 1926 and 1950 is explained first by natural erosion and second by dredgingErosion measured in the lower Mississippi River would have reduced Atchafalaya discharge had Atchafalaya Basin remained fixedDelta growth in the Atchafalaya Basin did not change partitioning, as it was downstream of a reach with steep water surface slope [ABSTRACT FROM AUTHOR]