The Dutch Aamsveen lies in a glacial basin in the Dutch-German border area. It consists of remnants of a cross-border raised bog and a lagg with degrading species-rich basiphilous plant communities. Farther west, the Glanerbeek drains the footslope at the edge of the basin and adjacent lagg. For the Netherlands, this is a rare wetland ecosystem and an important Natura 2000 area, but it is threatened by ongoing degradation. A spatiotemporal landscape ecological system analysis (LESA), including extensive palaeoecological research, showed the fundamental role of the interplay between infiltrating acid bog water that gradually acquires basic cations from the underlying base rich sediments as it flows laterally towards the lagg, where it seeps up, and the (lesser) influx of base rich surficial groundwater from the ice-pushed ridge in the west. Anthropogenic disturbance of this interplay has led to serious system degradation. The results of this LESA served to develop an integrated management plan at landscape level, instead of habitat level plans as is usual in the context of Natura 2000. This study illustrates the relevance of a spatiotemporal LESA for the recovery and sustainable management of such complex, dynamic systems.