In eastern part of the nature reserve there are 3 hiking trails in bogs and forests.

Männikjärve hiking trail. Length 3 km, duration up to 1.5 hours. Marked with red spots on the trees, there are several information boards on the trail. The trail runs in the forest around the shallow Lake Männikjärv, its shore is partly quaking. Starts and ends from Tooma village, Endla Nature Centers parking place.

If there are no time restrictions, you may pick wild berries, mushrooms and other natural products which are not under protection. Recreational fishing is allowed. On Lake Endla and Lake Sinijärv and Võlingi, Oostriku, Norra brooks fishing card is necessary, on other water bodies of Endla Nature Reserve, fishing is allowed with one simple hand line or recreational fishing rights apply (more information here). On water bodies no motorised vehicles are allowed. Bird hunting is not allowed in Endla nature reserve.

In the Endla Nature reserve, you must take into account several time restrictions to ensure peaceful nesting of the birds and spawning of the fish.

The State Forest Management Centre (RMK) engages the infrastructure for visitors in the nature reserves.  No accomodation or catering providers are in the nature reserve area, but you can find closest possibilitie from website Visit Estonia.

Bogs

About 10 000 years ago when the mainland ice receded Great-Endla Lake covered almost 3500 hectares of the Upland slopes. As the climate became warmer, swamps began to form in the lowest parts of the lakes. The 6 lakes of the nature reserve – Endla, Sinijärv, Männikjärv, Tulijärv, Kaasikjärv and Sinilaugas – are relict lakes of the Great-Endla Lake.

• Right of way: you can pass through and stay on private land from sunrise to sunset without causing disturbance to the owner or damage to the property. 
• If the private property is fenced or posted against trespassing, the landlord’s permission is necessary.
• You can use a non-propelled floating craft to move around internal water-bodies, except on bog lakes and Lake Kõnnu.
• It is permitted to drive your motor vehicle on public roads and pathways.

Iisaku nature centre  (located in the visitor’s centre of the Alutaguse National Park) has a permanent exhibition appertaining to the local nature and sustainable life-style of the area. Different study workshops are also available.

Alutaguse is a border area in many senses. Estonian, Russian and Votic cultures, languages and religions have met and mingled here throughout the centuries. Until the 14th century this area was mainly populated by Votes, with their large tumuli burial mounds situated in Jõuga. In the course of time Votes mingled with Russians at the Narva River and with Estonians in the middle of Alutaguse. An original ethnic group called Poluverniks  was formed in the vicinity of Iisaku, but they are now extinct.

The Smolnitsa Landscape Protection Area (250.6 ha) aims at the protection of the unique dunes of different ages on the northern shore of Lake Peipsi and their varied plant communities.This protected area, approximately 7 km in length and only 200–650 m in width, is a part of the Natura 2000 network and Alutaguse National Park.

The Mäetaguse oak forests and wooded meadows (53 ha) aims to preserve Mäetaguse Esker together with the forest on it, and to restore the semi-natural biotic community of a wooded meadow and a wooded pasture. The area is part of the Alutaguse National Park and Natura 2000 network.

The Jõuga Landscape Protection Area (310 ha) has been established for the protection of the relief, lakes and plant communities, which are unique and offer scientific interest. The area is a part of the Natura 2000 network and part of the Alutaguse national park. 

The formation of the Jõuga lakes took place about 12,000 years ago in the late glacial age. The development of lakes Jõuga started when huge blocks of ice, buried in sand and gravel, melted and, as a result, formed deep hollows.