Administratively most of the basin of the Bolshoy Anyuy and its tributaries belong to the Chukotka Autonomous Okrug of Russia.

It flows roughly westwards and passes through the sparsely populated areas of Chukotka, its valley forming the southern border of the Anyuy Range.

The Maly Anyuy joins it from the north near the Sakha Republic border and the combined river (now called the Anyuy) properly flows about 20 kilometres (12 mi) to meet the Kolyma at Nizhnekolymsk.

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