Rivers and lakes are very important part of the reserve uniqueness. At the territory of bordering Surqandaryo region and Tajikistan the glaciers of Severcev and Batirbay feed a great quantity of rivers. The widest rivers are Oksuv, Tarhoz and Kyzyldaryo. Merging in the Shahrisabz region these rivers form Kashkadaryo. Fed by glaciers, rainfall and ground waters, they create many waterfalls.
Main water source of Oksuv is river Tamshush. It starts from the rocks of Hodzhakulbars, at the height of 3500 meters above sea level. It is fed by snow, rain, and more than 32 of big and small streams.
Another major river is the water-bearing Tankhazdaryo originating at an altitude of 2700- 3500 m above the sea level, with a catchment area 459 km2, with 27 creeks such as Otatush, Ulugdara, Chot, Khodjakardon, Sarituz, Karangkul, Okdaryo, Kashkabulok, Kirkkiz and others. As a result of closeness of these inflows such settlements as Karakamar, Kosatarosh, Almaty, Shurkhasan, Kamar, Ommogon, Hitoy, Hazara and others.
The river Kyzylsuv is a major aquifer flowing through the reserve. It takes its start from the high snowy ridge Avgai Kalon, the height of which is 4000-4300 in above sea level. Its area of catchment is 650 km2, merging with creeks Kizilbulak, Kalasoy, Oksuv, Shilkhazor, Avgaikalon and others. The average width of the river varies from 10-30 meters, maximum depth is 2 meters and the length is 110 km.
Within the reserve there are 10 lakes of various sizes. 3 of them are located in Gilan, 3 - in Miraki, 1 - in Tankhozdaryo and 3 - in Kizilsuv sites.
Above mentioned rivers originate from the territory of the reserve and provide drinking water for 35-40 % of the population of Kashkadarya province. They irrigate the gardens, orchards, cotton plantations of Kitab, Shakhrisabz, Yakkabag, Chirakchi, Kamashi, Guzar, Karshi and Kasan regions.