The European Commission estimates that implementing the Habitats Directive and the Birds Directive throughout the EU requires 6.1 billion Euro a year. This includes costs of setting up the Natura 2000 network, managing sites, measures to maintain and improve the conservation status of protected natural habitat types and species, and success monitoring. Also included are expenditure under the headings of experiencing nature and environmental education. On a rough estimate, the amount of funding needed in Germany is some 620 Euro million a year.

Nature conservation measures in Natura 2000 sites can be funded in Germany through Länder programmes or by European funds under EU cofinancing arrangements. EU cofinancing for Natura 2000 in the 2007-2013 funding period is mainly provided through the European Agricultural Fund for Rural Development (EAFRD), the European Social Fund (ESF), the European Regional Development Fund (ERDF) and the LIFE+ financing instrument for the environment. The EU Commission has published a guidance Financing Natura 2000 Guidance Handbook setting out the EU funding options.

To make use of the EU funds, the German Länder must set up their own implementation programmes and have them approved by the EU. Information about the terms of funding is provided by the Länder nature conservation agencies.