According to the conservation policy of the Endla Nature Reserve, the main goal of the nature reserve is to protect, explore and present the well-preserved Endla mire complex, the karst springs of Pandivere Upland and the biodiversity there. The area of the nature reserve is divided into different zones. There is 1 strict nature reserve (9% of territory), 19 special management zones (65 % of territory) and 8 limited management zones (26% of territory).
Restrictions on activities are based on the Nature Conservation Act and the protection rules of Endla Nature Reserve (in Estonian). Works and activities are planned on the basis of is the management plan, the development document of the Endla Nature Reserve (for Years 2015- 2024 in Estonian).