Natura 2000

The Natura 2000 network aims to ensure the conservation and favourable status of habitats and species endangered across Europe


Natura 2000 is a pan-European network of nature reserves, the meaning and content of which are set out in the 1992 European Union Habitats Directive (92/43/EEC). The same directive also included bird areas selected under the Birds Directive (2009/147/EC), which entered into force in 1979, as part of the Natura network.


The number 2000 in the name of the network stems from the fact that, when the Habitats Directive entered into force, the Natura network was expected to be ready by the year 2000. In practice, twenty years later than planned, the selection of Natura sites is coming to an end, and all Member States are diligent in drawing up the management plans needed to plan the protection of the sites. The number in the title Natura 2000 is significant for us, because the establishment of the Natura network in Estonia started in 2000. That year, a national programme was approved, which ensured greater funding for nature conservation from the state budget, and the Natura pilot project in Lääne County and Rapla County began, which became a pioneer for the whole of Estonia.


Päikesetõus Alam-Pedjal
SUNRISE AT THE ALAM-PEDJA NATURA 2000 PROTECTED AREA. One of the most valuable parts of the Alam-Pedja nature reserve is the Emajõgi with its old rivers and grasslands. By: Igor Nael


Estonian Natura 2000 sites were selected by our accession to the European Union in 2004. Following the submission of the Natura sites, the European Commission analysed the adequacy of the sites submitted by us to protect all Natura habitat types and species listed in the Habitats Directive. As a result of the analysis, it became clear that we need to define additional natural areas for the protection of certain habitat types and species, whereas the selection of additional areas must take into account the so-called shadow list compiled by Estonian environmental organisations. The shadow list is drawn up by non-governmental organisations from all Member States and it brings together those areas which, in the opinion of non-governmental organisations, should be part of the Natura 2000 network in addition to the natural areas submitted by national institutions.


The adequacy of Natura 2000 sites submitted by Estonia was assessed in two stages: first for terrestrial, including coastal, habitat types and species (the corresponding boreal region seminar took place at the end of 2005), and later for marine habitat types and species (the corresponding Baltic Sea region seminar took place at the end of 2009). As a result of the Boreal Seminar, it was found that we have already selected enough areas to protect most habitats and species, but we were expected to protect additional areas with karst lakes, alvars and floodplain forests, pond bats, lady’-slipper orchids, and seven other habitat types and five other species. As a result of the seminar on the Baltic Sea region, we were expected to have at least one more area for the protection of sandy shoals and reefs.


Based on the above need, the original Natura 2000 sites were expanded and new sites were added to the network in spring 2009 and at the end of 2010. To date, the European Commission has estimated that we have enough Natura 2000 sites, but sites for individual species need to be added to the database.


At the beginning of the selection of Natura sites, there was a heated debate as to whether Natura sites should be small, well-defined along the borders of nature values – with one conservation zone being one Natura site – or whether Natura sites should be large, including both areas with nature values and the surrounding buffer zone. At the time, the leaders of the Natura pilot project decided to go with the advantages of large areas, which was certainly the right decision, especially given the great economic boom some time ago, during which all plots of land out of the scope of the Nature Conservation Act could have been exploited for construction.


The countries that went with small protected areas are now having trouble with how to ensure the ecological functioning of these areas and the movement of species between the areas. We, too, have the task of making the green network work better, so that, in the end, we have areas of sufficient size for nature to develop in its own right, and links between areas to ensure the necessary distribution routes for species – that is, the network.


The aim of the Natura 2000 network is to maintain or, where necessary, restore the favourable status of species and habitats endangered across Europe.


There are 60 habitat types in the Habitats Directive and 100 species in the Habitats Directive in Estonia, the protection and preservation of which Estonia must ensure. In accordance with Article 17 of the Habitats Directive, EU Member States, including Estonia, must submit a formal status report to the European Commission on the status of these species and habitats every six years. A methodological guide has been developed to determine the status of species and habitats. Based on that guide, all EU Member States assessed the status of habitats and species under the Habitats Directive for the first time in 2007, for the second time in 2013, and most recently in 2019, when the reporting period covered the years 2013–2018 [1].


Knowledge of the status of the species listed in the Habitats Directive in Estonia has improved year by year. Where we had 24% of species with an unknown status in 2007, there were 11% in 2013, and only 7% in 2019. The number of species in a favourable condition has increased, reaching 26% by 2007, 54% by 2013, and 56% by 2019. Compared to other European Union Member States, Estonian nature is in a relatively good condition. In the European Union as a whole, only 27% of all species reported are in a favourable position.


The status of the habitat types listed in Habitats Directive in Estonia has improved year by year. We had 42% of habitat types in a favourable condition by 2007, 52% by 2013, and 56% by 2019. In the European Union as a whole, only about 15% of habitat types are in a positive status.


Still, nearly half of the habitat types and species are in an inadequate or bad condition. This shows how many habitats must be restored, or just allowed to heal, in Natura areas. With restoration, close attention must be paid to, among other things, the restoration of semi-natural communities and the subsequent maintenance of restored communities, as 41,000 ha of semi-natural communities are currently maintained and restored with various subsidies, which is unfortunately not enough to achieve the favourable status of the communities and the species that live in them.


For the state of all species and habitats to improve in the future, nature conservation must be planned more accurately. Conservation management plans must be prepared for Natura sites, which state what natural values we hope to see in this area today, tomorrow, and in the distant future, i.e. the conservation management plan must set out specific conservation objectives.


As the Natura 2000 network is a common asset for the whole of Europe – each Member State has a responsibility to preserve its natural values for the whole of Europe –, the Habitats Directive also provides for European Union co-financing for the operation of the Natura 2000 network. Nature conservation may be financed from various EU funds. In Estonia, most funds come from the European Agricultural Fund for Rural Development, which provides 73 million euros for various grants in 2014–2020. It is used to support the maintenance of semi-natural communities and to compensate farmers and private forest owners for the loss of income due to restrictions in Natura sites. 53 million euros has been earmarked for nature conservation investments from the Cohesion Fund for 2014–2020. In addition, people can apply for funding for innovative projects with clear added value in a wider context from the environmental programme LIFE.


Preparations for the EU financing period 2021–2027 have begun. We hope that the need to finance the Natura programme is taken more into account in the future. This is the only way to ensure that the ambitious goal of the Natura 2000 network is met, which is the preservation of natural diversity in the long run, or, in other words, that all our species and their habitats are preserved and fully survive here when our great-grandchildren once walk around in Estonia.


The Estonian Natura 2000 sites have been established for the protection of 60 habitat types listed in the European Union Habitats Directive, 53 animal and plant species listed in Annex II thereof, and 136 bird species and migratory bird species listed in Annex I of the Birds Directive.


Natura 2000 does not mean that absolutely all areas where the habitat types and animal or plant species mentioned in the directives are present should be protected. Among the areas, the most representative part necessary for the preservation of the relevant species is chosen.


As at 2023, the Estonian Natura 2000 network includes 66 bird sites and 541 nature sites with a total area of 14,859 square kilometres [2].





Last modified: 28.09.2023





[2] Sirel, K. Pulk, E. 2020. Natura 2000 võrgustik. Roasto, R., Tampere, U. (toim). Eesti looduse kaitse aastal 2020. Keskkonnaagentuur, Tallinn: 28-31.