As a result of altered land use, water shortage and eutrophication, aquatic and semi-aquatic biodiversity in minerotrophic peatlands has severely declined in The Netherlands. After the improvement of surface water quality following hydrological and other measures, biodiversity is now increasing again in many reserves including former peat extraction areas, but not in all. In large peatland meadow areas, eutrophication is still a major problem and tightly linked to land subsidence. This paper reviews the current state of fen waters in relation to different restoration measures based on applied research, including projects sponsored by the Knowledge Network for Restoration and Management of Nature in The Netherlands. We also plead for more sustainable future land use and management of Dutch peatland areas, including marsh restoration and paludiculture, aimed at stopping land subsidence or at the regrowth of peat, and improvement of water quality.