In Tajikistan's dense river network, the largest rivers are the Syrdariya and the Amu Darya; the largest tributaries are the Vakhsh and the Kofarnihon, which form valleys from northeast to southwest across western Tajikistan. The Amu Darya carries more water than any other river in Central Asia. The upper course of the Amu Darya, called the Panj River, is 921 kilometers long. The river's name changes at the confluence of the Panj, the Vakhsh, and the Kofarnihon rivers in far southwestern Tajikistan. The Vakhsh, called the Kyzyl-Suu upstream in Kyrgyzstan and the Surkhob in its middle course in north-central Tajikistan, is the second largest river in southern Tajikistan after the Amu-Panj system. In the Soviet era, the Vakhsh was dammed at several points for irrigation and electric power generation, most notably at Norak (Nurek), east of Dushanbe, where one of the world's highest dams forms the Norak Reservoir. Numerous factories also were built along the Vakhsh to draw upon its waters and potential for electric power generation.

The two most important rivers in northern Tajikistan are the Syrdariya and the Zarafshon. The former, the second longest river in Central Asia, stretches 195 kilometers (of its total length of 2,400 kilometers) across the Fergana Valley in far-northern Tajikistan. The Zarafshon River runs 316 kilometers (of a total length of 781 kilometers) through the center of Tajikistan. Tajikistan's rivers reach high-water levels twice a year: in the spring, fed by the rainy season and melting mountain snow, and in the summer, fed by melting glaciers. The summer freshets are the more useful for irrigation, especially in the Fergana Valley and the valleys of southeastern Tajikistan. Most of Tajikistan's lakes are of glacial origin and are located in the Pamir region. The largest, the Qarokul (Kara-Kul), is a salt lake devoid of life, lying at an elevation of 4,200 meters.