The Zeya flows through theZeya Reservoir, at the junction of theTukuringra Range andDzhagdy Range, and joins theAmur nearBlagoveshchensk, at the border with China. Regulation of river discharge byZeya Dam mitigates extremities of river flow down to 5000 m³/s. The Zeya contributes around 16% of both the average and maximum flow of de Amur because of the flow regulations. In the past, the Zeya could have contributed up to almost 50% of the Amur's maximum flow of approximately 30,000 m³/s.
The river freezes from November to May. When it is unfrozen, the river is navigable with the most important river ports beingZeya,Svobodny, andBlagoveshchensk.