Several numerical challenges exist in the analysis of water-mooring line systems which require robust, yet practical, methods to address this type of fully coupled nonlinear dynamic problems. The present study proposes a novel class of numerical techniques for the formulation and implementation of a fully coupled dynamic system which involves water flows and catenary mooring line system. In particular, the three-dimensional water flow model is replaced by a simplified multilayer shallow water system with mass exchange terms between the layers including frictional forces at the bed topography and wind-driven forces at the water free-surface. Coupling conditions between the multilayer shallow water model and the mooring line system are also investigated in the current work. As numerical solvers we implement a fast finite volume method for the multilayer shallow water equations and a nonlinear dynamic analysis for the mooring line based on elastic catenary cable elements. Efficient calculations of the interaction forces between the shallow water flow and the submerged mooring line system and associated numerical implementations are also discussed. The accuracy and computational advantages of the proposed fully coupled system are verified using a series of well-established benchmark problems and wind-driven flows over both flat and non-flat beds. The computational results obtained show high performance the developed model and demonstrate the ability of the method to simulate fully coupled dynamic water-mooring line systems.