Climate change and atmospheric nitrogen deposition can impact the integrity of ecosystems. Therefore, the EU Biodiversity Strategy foresees that Member States map and assess the state of ecosystems and their services in their national territory. By example of Germany, this article presents a quantitative, spatially explicit as well as nationally, regionally and site-specifically applicable methodology for classifying and mapping forest ecosystems and identifying changes of their integrity comparing their reference states (1961-1990) with measured (1991-2010) und potential future conditions (2011-2017). To this end, measured environmental data were complemented by dynamic modelling of future climate and soil conditions. A fuzzy rule-based model for estimating spatial patterns and temporal trends of soil moisture was developed and tested at the federal and regional level. Forest ecosystem conditions were evaluated and ordinated at three levels (indicators, functions and ecosystem type) with regard to functionality, chemical and biological characteristics, stress tolerance against climate change and nitrogen deposition scenarios for the years 1961-1990, 1991-2011 and 2011-2070.