Three teenagers have landed themselves in hot water on Melbourne's Yarra River this morning after being arrested for allegedly attempting to steal a water taxi.

Witnesses called police after seeing two boys standing on a boat as it drifted down the river with no lights on at around 4.30am.

Another boy was seen running from the area when onlookers tried to intervene.

Two teenagers were taken to hospital after being pulled from the water. Picture: 9NEWS (9news)

Two boys were seen standing on a boat as it drifted down the river. Picture: 9NEWS (9news)

A 16-year-old and a 13-year-old are being treated in hospital after being pulled out of the river.

An 18-year-old was taken into custody but has since been released.

Another boy was seen running from the area when onlookers tried to intervene. Picture: 9NEWS (9news)