The river was improved with the addition of 15 locks between Ipswich and Stowmarket to form the Ipswich and Stowmarket Navigation, although this name has fallen out of use. The navigation was established by two Acts of Parliament in 1790 and 1793. Recently, the navigation has undergone restoration.
In the year 860 the Danes sailed up the river and established the village of Rattles-dane near the source of the River Rat. From this village now known as Rattlesden they attacked the Saxon stronghold of Haughley Castle. Stowmarket, a few miles South of Haughley, was of little significance then.
In 1065 Caen stone for Bury St. Edmunds Abbey was imported from Normandy and transported in flat-bottomed boats to Rattlesden. Stowmarket church bells were re-cast in the l7th century after being transported down-river.
The first proposal for the construction of the navigation was in 1719, but the traders of Ipswich objected, fearing loss of trade. It was not until 1789 that six local gentlemen (two of whom were vicars) with foresight realised that because of poor transport, due to badly-maintained turnpike roads, the population and industries were dwindling in the Stowmarket area. They engaged William Jessop, who employed Isaac Lenny as the surveyor and a Parliamentary Bill for the construction of the navigation was passed on 1 April 1790. A Board of Trustees was appointed to manage the waterway, which was expected to cost £14,300.
Work started that year at the Ipswich end but the contractors Dyson and Pinkerton were dismissed due to problems with trespass. A local contractor was employed to continue work at the Stowmarket end and in 1791 John Rennie was consulted. He reported that three turf and timber locks had been constructed between Stowmarket and Needham Market, the other main town on the waterway, advised that further lock structures should be of brick and stone and estimated costs to complete the works. This amount was raised by a Parliamentary Bill of 28 March 1793. The final cost of construction was £26,263, which was nearly double the original estimate.
The navigation was completed in 1793 and three barges loaded with coal made the 17 mile trip from Ipswich to Stowmarket on September 14th, rising 90 feet through 15 locks of broad construction each 55ft by 14ft, the draught being 3.3ft.
The Ipswich to Stowmarket railway line opened in 1846, and with it came a serious decline in traffic on the navigation. Under the terms of the authorising act of Parliament, the Board of Trustees had legal obligations to maintain the waterway, but by 1932 they were unable to meet these, as there was no income from traffic. They therefore applied for a Revocation Order, which was granted, and the Board ceased to exist after 1934. The waterway gradually fell into decay.
Claydon lock was destroyed when the A45 road was built. The river at this point was diverted through a new cut, and the site of the lock lies under the road, which has now become the A14 trunk road.
Water levels on the river are regulated by various devices. Hawks Mill lock at Needham Market has had an automatic rising sluice gate fitted, while Paper Mill lock incorporates an automatic tilting sluice gate.