The combination of brackish and freshwater habitats makes Škocjanski zatok a very diverse environment, regardless its small area. Nearly three quarters of the nature reserve is covered by the brackish lagoon – its nesting islands, saltmarshes and mudflats are a home to a range of rare animal and plant species. The best known among the plants are the halophytes, plants adapted to the salt in the air and soil, which in Slovenia next to Škocjanski zatok only grow in Sečovlje and Strunjan Nature Parks.
The freshwater part of the nature reserve is located in Bertoška bonifika. It was artificially created during the reserve restoration in 2006-07 as a substitute habitat for the wetlands lost nearby Koper through the urbanisation processes in the past decades. It consists of wet meadows, reedbed and deep water areas which are all important breeding and feeding grounds for birds.
Birds are the most outstanding fauna group: a reserve area of only 122 hectares hosts 259 species and the number is still increasing. This is over 60% of all bird species observed in Slovenia. The diversity of birds is a direct positive result of the carefully planned and implemented restoration and management of the reserve. Due to the extremely positive impact to the reserve’s biodiversity increase, the restoration is considered one of the biggest success stories of modern nature conservation in Slovenia.