The Whangae River is a short river of the Northland Region of New Zealand's North Island. It flows generally northeast to reach a southwestern arm of the Bay of Islands. The estuary is about 2 km (1.2 mi) and the river about 5 km (3.1 mi) long. Like much of the coast north of Whangārei, the valley is formed of Waipapa greywacke.

The Whangae River Estuary is designated as an area of Outstanding Natural Character, due to its railway causeway (now followed by the Pou Herenga Tai – Twin Coast Cycle Trail) and its tall mangroves (mānawa), which give way up river to saltmarsh. Bush covers much of the valley, mainly taraire-puriri forest with emergent rimu, rewarewa and occasional totara, pukatea, kahikatea and kauri. More tōwai grow towards Opua. There are also areas of manuka, kānuka, tanekaha, kohuhu. five finger (puahou), mamaku, patē, hangehange, cabbage tree (tī), cutty grass and raupō, with Northland green gecko (kawariki), tomtit (miromiro), brown kiwi, weka, kererū and kōtātā.

From 14 August 1931 to 1 September 1963 there was a Whangae Bridge flag railway station.

• List of rivers of New Zealand

• "Place name detail: Whangae River". New Zealand Gazetteer. New Zealand Geographic Board. Retrieved 12 July 2009.

35°20′S 174°06′E / 35.333°S 174.100°E / -35.333; 174.100