Until the 13th century, the river flowed via Upware and Wisbech but then changed its course to come out at King’s Lynn. The river became important for trade and from the 17th century improvements were made to the navigation. At the same time, drainage works were carried out in the area. By the early 20th century, navigation had ceased upstream of St Ives, but the Great Ouse Catchment Board reopened navigation to Godmanchester and then Eaton Socon just before the Second World War. The navigation was reopened to Bedford in 1978, following a campaign led by the Great Ouse Restoration Society, and supported by IWA, with volunteer support from Waterway Recovery Group.
There is a detailed history of the river in Wikipedia.