The terrestrial SPA network is almost complete. Enlargements are foreseen, but are not major.

However, completeness of the terrestrial SCI network in Estonia is lower than for SPAs.Several habitat types, such as Nordic Alvars, and some types of forests are not sufficiently covered.

The protection status of existing sites is generally sufficient. More than 95% of the total area of existing Natura 2000 sites is covered by national designations.

The protection regime of some sites does not sufficiently avoid human pressures. Management planning has progressed well, but the plans still have low site coverage and there are gaps in their implementation.

Appropriate assessment according to art 6 of the Habitats Directive is routinely used, but the quality of the assessments is moderate.

Data on total costs is not available. European funds are used mainly for financing management/action planning of sites/species, for active management of semi-natural habitats and to subsidise owners for conservation of Natura 2000 forest habitat types.

Efficiency of LIFE is remarkable although this project-based instrument has certain limits. National funding to cover the actions foreseen in Species Action Plans and site management plans is insufficient.

Work on Master Action Plan on Nature Conservation (can be classified as a Prioritised Action Framework) has progressed well.