Under Article 6 (3) of the Habitats Directive and Article 34 of Germany’s Federal Nature Conservation Act, all plans (e.g. building and construction) and projects (e.g. a new motorway) which either by themselves or in combination with other plans or projects, are likely to have a significant effect on a Natura 2000 site (protected under the Habitats Directive or the Birds Directive) shall be subject to appropriate assessment of its implications for the site in view of the site's conservation objectives.

This means that such plans and projects are subject to a preliminary impact assessment, where existing documentation is used to assess whether they are likely to have significant adverse effects on a Natura 2000 site. If such effects can be ruled out, a detailed assessment is no longer required. The reasoning for the decision must however be adequately documented. In all cases, it is immaterial whether the plan or project in question has a direct effect on components of a Natura 2000 site or affects them indirectly from elsewhere. If uncertainties remain as to whether significant adverse effects can be completely ruled out, an impact assessment as called for under Article 34 ff of the Federal Nature Conservation Act must be performed to provide clarity. Strict adherence to the precautionary principle is required when conducting the assessments so that the mere likelihood of significant adverse effects gives rise to an obligation to conduct a full-blown impact assessment.

The impact assessment is conducted on the basis of the conservation objectives agreed for the respective site. The key issue is whether a project or plan can have significant adverse effects on a Natura 2000 site given the site's conservation objectives. The assessment thus covers:

The decisive assessment phase of an impact assessment involves evaluation of the significance of the effects. The level of significance can only ever be identified on a case by case basis using criteria such as scope, intensity and duration of the adverse effects. In legal terms, the issue at hand is whether a plan or project can have significant adverse effects and not whether it can be proven that they will actually occur. An adequate likelihood of the occurrence of significant adverse effects suffices for a plan or project to be deemed inadmissible.

In practice, determining the level of significance is a key problem. BfN therefore commissioned a research and development project in 2001 to determine what constitutes significant adverse effects within the meaning of Article 34 of the Federal Nature Conservation Act. The project findings were published in a report (Lambrecht et al. 2004). Among other things, the report proposed a set of practical conventions for assessing the significance of adverse effects upon direct appropriation of land from habitat types protected in line with the conservation objectives of a Natura 2000 site or from habitats of animal species. In the years that followed, these conventions were evaluated, updated from new data on proposed sites and refined methodologically in a broad-based, multiple-phased consultation and coordination process. The revised version of the  proposed conventions (Lambrecht † and Trautner 2007, in German) provides a method for assessing significance from a conservation standpoint based on current scientific knowledge. It serves as a valid, discerning framework for guiding the assessment of individual habitat losses.

If a project or plan either by itself or in combination with others has significant adverse effects on specific components of a site which are key to its conservation objectives, approval may be granted as an exception and subject to a special impact assessment under Article 34 (3) and (5) of the Federal Nature Conservation Act:

Because Article 6 plays a key role in site management and administration, the European Commission has issued a guide to assist in its interpretation:  Managing Natura 2000 Sites: The provisions of Article 6 of the Habitats Directive.