It has a total length of about 505 kilometers and a catchment area covering 27.753 square kilometers. It is located in the Cagayan Valley region in the northeastern part of the island of Luzon. Its main tributaries are the Pinacanauan, Chico, Siffu, Mallig, Magat and Ilagan rivers.
The Cagayan River and its tributaries are prone to extensive flooding during the monsoon season, which in Southeast Asia lasts from May to October. In November 2020, after Typhoon Vamco (known in the Philippines as Typhoon Ulysses) hit, the river peaked and caused flooding in its vicinity. It was one of the worst floods in the river's history.
The Cagayan flows through one of the few remaining primary forests in the Philippines. It supports the lives of many endemic and endangered species, such as the Luzon bleeding-heart (Gallicolumba luzonica ), the Philippine eagle (Pithecophaga jefferyi), and the rare river fish, locally known as Lobed River Mullet (Cestraeus plicatilis).
