The fluid dynamics of channel confluences are highly complex due to flow separation and secondary currents. Although numerous studies in the past few decades have focused on the numerical simulation of confluence flow, deformed beds were rarely used. This study attempts to address this issue through numerical simulation of the flow behavior in an open-channel confluence flume with an equilibrium degraded bed in OpenFOAM (version 6.0) to compare the results with a flatbed. In the present study, different turbulence models, including Reynolds-Averaged Navier–Stokes (RANS), large-eddy simulation (LES), and detached eddy simulation (DES) models were performed using rigid-lid and volume-of-fluid (VoF) methods. The accuracy of the models was statistically analyzed by comparing them with observation data. The results demonstrated that the LES model had the best performance, with a minimum average normalized root-mean-square error (NRMSE) of 3% under the VoF assumption. The investigation also further illuminated the intricate interplay of vortical structures within the confluence zone. Notably, the number and behavior of vortices were found to be influenced by channel geometry and size, as well as interactions between separated shear layers. Circulation within the separation zone near the inner bank differed in rotation between the degraded and flatbed cases.