An interdisciplinary study was carried out to trace the hydrological changes of the Havel River in northeastern central Europe over the last ca. 2000 years. This research was driven by the hypothesis that the present‐day riverscape is to a large degree a result of medieval and modern human transformation of the drainage system. The river system forms a series of dammed lakes and river sections that were greatly altered through hydraulic engineering in the past. Along the middle course of the Havel, 16 sedimentary sequences available for geoarchaeological and paleoecological research were analyzed in order to reconstruct regional water level dynamics. Chronological control was ensured through a multitude of palynological, dendrochronological, archaeological, and radiocarbon data. The sections upriver from the Brandenburg/H. and Spandau weirs, representing sites with historic watermills, reveal substantial water level changes during the late Holocene. Generally, lower water levels before and higher levels during the medieval German colonization of that area (ca. A.D. 1180/1250) can be inferred. This water level increase, which is primarily attributed to dams constructed for watermills and secondarily due to a multitude of fish weirs, took place rapidly and amounted to a relative height of ca. 1.5 m. It enlarged the river's cross‐sections and increased the size of existing lakes or initiated secondary lakes that previously aggraded, and thus caused flooding of large parts of land. The rising water level even influenced the settlement topography to a large degree. Several medieval rural settlements were abandoned due to flooding. In total, a ca. 150‐km long dammed lake cascade was formed.