The area of Škocjanski zatok is designated a nature reserve from 1998 upon the Act on Škocjanski zatok Nature Reserve, adopted by the Slovenian Parliament (Official Journal of RS, no. 20/98). The level of protection corresponds to the IUCN category IV.
In Škocjanski zatok Nature Reserve it is not allowed to:
- Intake of the sewage water, water from industry and liquid waste;
- Worsen the water and soil quality;
- Change the water regime;
- Construct buildings and machninery;
- Deposit waste;
- Pollute the air with emissions from within the reserve;
- Use agrochemical fertilisers and other matters for plants;
- Dig, collect or damage plants or destroy vegetation;
- Change coastal vegetation;
- Hunt, collect, disturb or kill animals in all development stages;
- Destroy or damage breeding sites and areas where the animals feed, reproduce or rest;
- Change the form and composition of the surface;
- Cause noise, explosions or vibrations and artificially illuminate the animals and their habitats;
- Use of vehicles and boats;
- Visit the reserve contrary to the rules for visitors
Exceptionally, some of those activities are allowed for the reserve manager when implementing the management of the area upon the Management Plan.
Visitors are not allowed to enter the brackish lagoon with surrounding habitats and a small area of Jezerce along the railway. Land use change is not permitted, with the exception of the construction of the foreseen visitor facilities at the border of this area and reserve management.