Thus, the European network of protected sites is challenged by anthropogenic actions and climate change (CC). Nature conservation agencies have to cope with modifications of habitat composition induced by CC and the fact that the targeted conservation may no longer be valid. Scenarios and indicators applied for the local scale are missing and likewise there is a lack of knowledge. The direction of future changes and how this matches with a long-term impact of management measures are unclear. At site-level, precipitation might de- or increase and shift its seasonality, leading to different preconditions for the remaining natural habitats, especially water-based ecosystems such as wetlands and rivers but also the composition of forested areas and grasslands. The main challenges are to monitor changes through time (history, present state, short term future, long term future) and to adapt management strategies and to consider flexible responses to ongoing developments.