The western edge of the Alutaguse region extends up to the eastern foot of the Pandivere Upland. The latter is characterised by a belt of well fed springs, which are the sources of the largest rivers of Alutaguse. The rivers belong to three different catchment areas. The Avijõgi, Rannapungerja, Tagajõgi, and Alajõgi Rivers drain into Lake Peipsi; the upper stream of the Purtse (Oandu) River, flows into the Gulf of Finland; the Mustajõgi and Poruni (Borovnja) Rivers discharge on the eastern edge of Alutaguse region into the Narva River, the largest river in Estonia.

The latter has numerous oxbows or ana-branches at its source. There are also two relatively deep valleys here: Poruni is a primeval valley, with many rock outcrops, cut into the Narva sandstone and domerite layers; the Rannapungerja Valley is the deepest valley in North Estonia which has cut only through the earth's surface layers.

There are many lakes in the Alutaguse region, but they are unevenly distributed. The largest concentration of lakes is in the Kurtna Kame Field, but there are plenty of lakes within the Iisaku-Jõuga-Illuka esker range (the Jõuga and Kõnnu Lakes). The lakes situated deep in mires, such as Arvila (Ratva), Tudu and Imatu Lake, and the Puhatu lakes, are also worth mentioning.

Kurtna lakes include 40 lakes of different sizes and depths, and with different hydrobiological characteristics. Some of the lakes are linked by canals, ditches, or streams. The largest of them are Konsu, Kurtna Suurjärv, Jaala, Räätsmäe (the only iron-rich lake in Estonia), Suur Kirjakjärv, Väike Kirjakjärv, and Valgejärv (where the plant rarity — water lobely — Lobelia dortmanniana — grows).

Mires are a natural part of the Alutaguse landscape. Estonia's largest mire system — Puhatu, which combines smaller mires such as: Krivasoo, Agusalu soo, etc., is situated here. The western part of the landscape region includes the protected Muraka and Ratva Bogs and Sirtsi Mire. Tudu Punasoo Mire and Luusaare Bog lie even further to the west.

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