Background Situated between the harbour and the centre of the city of Koper, the third largest city in Slovenia, the Skocjanski zatok nature reserve is the only large brackish wetland in the country. Thirty years ago the brackish lagoon, with its shallow water areas and mudflats, its reed beds and meadows, provided food and shelter for 41% of all amphibian and reptile species and 55% of all bird species in Slovenia. But the area was transformed into an industrial and commercial centre. The Badasevica river was diverted from the lagoon to a nearby bay and the area was used as a disposal site for mud extracted to expand the port capability. Industrial development resulted in a drastic loss of habitat and species. The breeding population of the little bittern (Ixobrycus minutus), for instance, dropped from 16 to three pairs. In 1993, however, a temporary act put a halt to the destruction of the site and started a process which led to the creation of a nature reserve in 1998. The following year the Slovenian parliament approved a five-year action plan for the protection and development of the area. In September 1999, following a public tender, DOPPS-Birdlife was granted a ten-year license for the management of the reserve, the first case in Slovenia of a NGO managing a protected area. Objectives The main actions of the project, which form part of a larger programme aimed at reducing the levels of pollution, are directed at restoring habitats important for the survival of bird species. Such restoration would be done by improving the lagoon's water circulation, through the removal of sediments, the creation of a new marsh, flooding an area previously used for agriculture and the installation of equipment to control and regulate the inflow and outflow of water. At the conclusion of the project a detailed management plan of the site would be approved and adopted. DOPPS-Birdlife planned to seek community participation in the practical aspects of restoring the lost habitats by encouraging local voluntary work, organising public meetings and providing information in the form of a video and a brochure. Results The project has substantially contributed towards establishing a favourable conservation status of habitats and birds in Škocjanski zatok. The habitats, which are recognised as rare and endangered on a national and EU level, have been restored and enhanced, thereby ensuring favourable conditions for the increase in the number of species and populations of important birds in the reserve. Škocjanski zatok has been designated a Natura2000 site containing the following protected bird species: Kentish plover (Charadrius alexandrinus), little bittern (Ixobrychus minutus), great reed warbler (Acrocephalus arundinaceus), reed warbler (Acrocephalus scirpaceus) and five habitat types listed in the Annex I of the Habitat Directive. After the completion of the freshwater habitat, a number of breeding pairs were monitored; all together 204 bird species were recorded in the summer of 2007. The restoration of the lagoon ensured that the conservation and legal goals of the Natura2000 were met. The new mudflats and islets will give new additional grounds for three targeted habitat types, which were destroyed during the past degradation: Salicornia and other annuals, Mediterranean salt meadows (Juncetalia maritimi) and Mediterranean and thermo-Atlantic halophilous scrubs (Sarcocornetea fruticosi). The priority habitat type, ‘coastal lagoons’, covers all the water parts of the lagoon. Additionally, the Ara channel mouth area has a good potential to develop into the habitat type, ‘estuaries’. Though the Škocjanski zatok nature reserve is located in a densely urbanised area, residents of the town of Koper need green areas for recreation and many of them recognise the value of and contribute to the conservation of the area. The reserve is an environmental education resource of benefit to local schools, education establishments, and scientific and research centres. The reserve has also added to the value of Koper as a tourist destination. Finally, the project is a demonstration of good nature conservation practice and it positively influences national environmental policies and initiatives. The Program of the Protection and Development of Škocjanski zatok NR for the period 2007-2011 published in the Official Journal Republic of Slovenia provides a good basis for future management and progress. The expected construction of visitor facilities (visitor centre, central bird-watching hide, bird-watching tower, educational trails) by the end of 2009 will help deliver the centre’s key messages. Further information on the project can be found in the project's layman report (see "Read more" section).