Its territory consists mainly of an extensive plain at an altitude up to 300 m (980 ft) above sea level, with a number of depressions and highlands (Sultanuizdag, Bukantau).

The area of the reserve amounts to 101,000 km2 (39,000 sq mi) and it is located on flood-land (tugai) drained by the Amudarya close to the settlement Dargan Ata.

Fauna include: Bactrian deer (Cervus elaphus bactrianus), wild boar (Sus scrofa), common pheasant (Phasianus colchicus), golden eagle (Aquila chrysaetus).

Of particular interest is the Bissekty Formation of Uzbekistan, from the early Late Cretaceous, which has produced several species of early birds: Incolornis martini, Explorornis walkeri, Kizylkumavis cretacea, Kuszholia mengi, Lenesornis kaskarovi, Sazavis prisca, Zhyraornis kaskarovi and Z. logunovi are recognized as valid species.

[2] Other fossils from the Cretaceous rocks of the Kyzylkum include tree trunks, pelecypods, beetles, sharks, rays, bony fish,[3] frogs, salamanders,[4] turtles,[5] crocodylomorphs,[3] pterosaurs,[6] and a varied fauna of small early mammals.

[2] The local population uses the large spaces of the Kyzylkum Desert as a pasture for livestock (mostly sheep, Bactrian camels and dromedaries).