Central European urban regions are challenged by urban sprawl and suburbanization as well as by the reluctance of investors to take on urban brownfield locations. Poorly integrated and unsystematic land use, development policies and environmental management regulations increase land–related conflicts, handicap economic development, undermine social cohesion and effects region’s competitiveness. There is a need to find ideas for interregional cooperation, tools and instruments to resolve the problems while respecting territorial sovereignty and reflecting the problem of fuzziness of the territorial units. An integrated approach is needed where multiple actors can participate and cooperate in territorial and environmental management to develop their regions. As one of the most challenging topics of environmental management of land resources is the disparity present in the territorial governance, the objective is to strengthen the functional ties, integration and cooperation between the core city and surrounding municipalities and to achieve sustainable land use by sound environmental management. The innovative solution have to provide an integrated territorial and environmental approach, also by including new concepts of ecosystem service management. A possible solution to ease these complex problems is to develop integrated environmental strategies in functional areas connecting urban and peri-urban level beyond Administrative Urban Areas in Functional Urban Areas with links to local and regional scale. This way, environmental and spatial decision levels are bundled by a Functional Area Management Strategy (FAMS). FAMS would include traditional planning strategies and innovative internet based stakeholder participation. The ecosystem service concept can support the assessment and decision-making process. This innovative approach, integrating ecology and economics to help explain the effects of spatial development policies and impacts both on ecosystem properties and on human welfare seems to be crucial for the use of space not only as efficient as possible but also for safeguarding its sustainability.