[3] During the time of the Assyrian rule over the country, a fortress was built in a site known today as Tell Qudadi, on the northern bank of the river, next to its estuary.

On 27 April 750, the Abbasid general Abd Allah ibn Ali, uncle of Caliph al-Saffah (r. 750–754), marched to Antipatris ('Abu Futrus').

There, he summoned around eighty members of the Umayyad dynasty, whom the Abbasids had toppled earlier that year, with promises of fair surrender terms, only to have them massacred.

[4] In 975, the army of the Egypt-based Fatimid caliph al-Aziz defeated and captured the Aleppo-based Hamdanid general Aftakin on the banks of Auja.

[2] The Arabic name of the river, al-Auja ("the meandering one"), is shared with Wadi Auja, another small stream that flows into the Jordan Valley north of Jericho.

[8][page needed] In 1930s, the British authorities in Palestine searched for an additional major water resource for the evolving city of Jerusalem.

When the river's headwaters were diverted to the Negev via the National Water Carrier for irrigation purposes, the state of the Yarkon declined.

[10] Subsequent and ongoing cleanup projects, some government-run, some benefitting from financial aid from Jewish donors from Australia, and some with regional character supported by the NGO FoEME, helped improve the quality of the water.