Climate change impacts on individual species are various and range from shifts in phenology and functional properties to changes in productivity and dispersal. The combination of impacts determines future biodiversity and species composition, but is difficult to evaluate with a single method. Instead, a comparison of mutually independent approaches provides information and confidence in patterns observed beyond what may be achieved in individual approaches. Here, we carried out such comparison to assess which ecosystem types in the Netherlands appear most vulnerable to climate change impacts, as arising from changes in hydrology, nutrient conditions and dispersal limitations. We thus combined meta-analyses of species range shifts with species distribution modelling and ecohydrological modelling with expert knowledge in two respective impact studies. Both impact studies showed that nutrient-poor ecosystems and ecosystem types with fluctuating water tables-like hay meadows, moist heathlands and moorlands-seem to be most at risk upon climate change. A subsequent meta-analysis of species-environmental stress relations indicated that particularly endangered species are adversely affected by the combination of drought and oxygen stress, caused by fluctuating moisture conditions. This implies that adaptation measures should not only aim to optimise mean environmental conditions but should also buffer environmental extremes. Major uncertainties in the assessment included the quantitative impacts of vegetation-hydrology feedbacks, vegetation adaptation and interactions between dispersal capacity and traits linked to environmental selection. Once such quantifications become feasible, adaptation measures may be tailor-made and optimised to conserve vulnerable ecosystem types. © 2013 Springer-Verlag Berlin Heidelberg.