The intensity and frequency of natural hazards such as landslides, debris flow and mud flows have increased significantly over the last years due to climate change and global warming. These catastrophic events are responsible for numerous destructions of infrastructures and landscapes and often even claim human lives. Therefore, in addition to the prediction, the design and installation of protective structures are of tremendous importance. In recent decades, highly flexible protective structures have been favoured due to their enormous energy absorption capacity while adapting well to the environment. However, the dimensioning of such protective structures is a very complex task that requires advanced numerical simulation techniques. In order to capture the behaviour of such natural hazards on one hand and the highly flexible protection structures including complex elements as sliding cables or brakes on the other hand, a partitioned coupling approach is proposed in this work. In this way, the most appropriate solvers, treated as black-box solvers, can be selected for each physics involved, while the interaction is shifted to the shared interface. The Material Point Method (MPM) is particularly well suited to capture flow processes with large strains and time-dependent material behaviour due to its hybrid approach of an Eulerian background grid in combination with Lagrangian moving integration points. At the shared interface non-conforming essential boundary conditions are introduced within the MPM model to reflect the behavior of the flexible protective structures. These, in turn are modelled using the Finite Element Method (FEM) to capture the advanced structural model behavior, receiving the impact forces at the shared interface as external loads. Consequently, a Gauss-Seidel iteration scheme is applied exchanging the interface conditions for the equilibrium at the shared interface.