Integrated ecological information systems are characterized by a broad range of thematic spatial data layers and a variety of specific application areas. Monitoring and management tasks differ widely and cover scales from local to continental. In European Nature Conservation the implementation of the habitat directive (92/43/EEC), the bird directive (79/409/EEC) and the Natura 2000 network requires a harmonized monitoring and management of the designated protection areas. This task challenges local authorities responsible for the individual sites as well as authorities on the national and EU level that are in charge of the assessment and channelling of the huge data flow arising with observation, documentation, and control mechanisms from the local sites. Environmental information systems with integrated Earth Observation (EO) will provide an essential contribution to the monitoring of NATURA 2000 sites and other protected areas of European importance beyond established mapping and classification approaches. Data streams from EO data processing and field ecological work will converge in an operational Geographic Information System (GIS) with a harmonized design but open to regional specifications. First case studies across Europe highlight the enormous stimulus of EU legislation on the development and harmonization of environmental monitoring and management procedures.