The Darss-Zingst Peninsula on the southern Baltic Sea was formed after the Littorina transgression onset about 8000 cal. y BP. It originated from several discrete islands, has been reshaped by littoral currents and wind-induced waves during the last 8000 y, and evolved into a complex lagoon system as seen today; thus, it may serve as an example to study coastal evolution under long-term climate change. A methodology for developing a multiscale process-based morphodynamic model for simulation of decadal to centennial evolution of a wave-dominated coastal environment is presented here. The model consists of eight main modules. The two-dimensional vertically integrated current module, the wave module, the bottom boundary layer module, the sediment transport module, the cliff erosion module, and the nearshore storm module are real-time calculation modules that aim to solve the short-term processes. A bathymetry update module and a long-term control function set, in which the “reduction” concepts and techniques for acceleration of morphological update are implemented, are integrated to extend the effects of short-term processes to a longer-term (yearly) scale. Successful model validation demonstrates that it is capable of simulating the long-term morphological evolution of the southern Baltic coast. Model results indicate that coastline change of the Darss-Zingst Peninsula is dominated by mechanisms that act on different timescales. The coastlines of Darss and Hiddensee Island are mainly reshaped by long-term effects of waves and longshore currents, while coastline change of the Zingst area is a combination of long-term effects of waves and short-term effects caused by extreme wind events.