The Agauntza River is born in Ataun and poured its waters into the Oria River in Beasain. This river, which is born in the area of Lizarrusti and runs through the 15 kilometres of Ataun, collects the waters of many streams.

With regard to water, in addition to the importance of the aquifers of the Dome of Ataun, it is necessary to mention the aquifers of other areas of Aralar. In fact, in Aiaiturrieta, the most important spring of Ataun, both the waters to the south of the Dome and the waters to the south of the Sierra de Aralar emerge. It should be borne in mind that some of the waters of Aiaiturrieta are intended for human supply.

The Lareo reservoir also stands out. Although it is located on land in the Enirio-Aralar Commonwealth, both access to it and the flow of its flows directly communicate with Ataun.

In addition, there are other important streams in Ataun. Like the aforementioned Aitzarte and Kobatxo that cross the border of the Dome or the Lauztierreka Creek that extends west of the San Gregorio neighborhood.