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Improving current understanding of hydrodynamics and sediment dynamics in complex tidal embayments is of major importance to face future challenges derived from climate change and increasing human pressure. This work deepens the knowledge of the hydro-morphodynamics of complex creek networks that connect basins with different characteristics, identifying their morphodynamic trends and the potential impacts of channel deepening. We selected two tidal creeks which flow through salt marshes and tidal flats of the Cadiz Bay (SW Spain) in a singular network due to their double connection to the Atlantic Ocean and the inner bay. We study the interactions between tidal waves that penetrate into the creeks from these two different bodies of water, analyzing the tidal asymmetry and the morphodynamic tendencies of the system. For the analysis, we set up a hydro-morphodynamic model specifically developed for areas with very shallow and complex channels. Results show that the tidal wave penetrates within the tidal network both from the inner Bay and the open ocean with different amplitudes, phases and flow velocities. There is also an asymmetric pattern for the tidal flows caused by the deformation of the dominant astronomical tidal constituents, M2 and M4, due to the non-linear interaction of tidal currents with the irregular creek geometry and bottom topography. Tidal asymmetry promotes the progressive infilling of the area where the tidal waves meet closing the connection between the open ocean and the inner bay, such an infilling trend being accelerated by human interventions.