In this paper, we unravel the mechanisms responsible for the development of the two-channel system in the Outer Weser Estuary. A process-based morphodynamic model is built based on a flat-bed approach using simplified boundary conditions and accelerated morphological development. The results are analyzed in two steps: first, by checking for morphodynamic equilibrium in the simulations and second, by applying a newly developed method that interprets simulations based on categorization of the two-channel system and cross-sectional correlation analysis. All simulations reach a morphodynamic equilibrium and develop two channels that vary considerably over time and between the simulations. Variations can be found in the location and depth of the two channels, the development of the dominant channel over time and the alteration in the dominance pattern. The conclusions are that the development of the two-channel system is mainly caused by the tides and the basin geometry. Furthermore, it is shown that the alternation pattern and period are dependent on the dominance of the tides compared to the influence of river discharge.