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The first meeting of the new company took place on 19 April 1790, and William Jessop was asked to prepare drawings which would form the basis for tenders. The directors also decided to advertise for a surveyor, and on 7 June they appointed James Smith from Reading. They expected the navigation to be finished by October 1791, and so Smith's contract only ran until then. At the same meeting they appointed Mr Baynes of Stowmarket to handle legal matters, and Dyson and Pinkerton as contractors. Both were members of civil engineering families, whose careers had developed since the 1760s, and who had collaborated on a number of schemes, making them the first civil engineering contractors. John Dyson Sr had worked with James Pinkerton on the Adlingfleet Drainage scheme, the Driffield Navigation and the Laneham Drainage scheme, but for this project, he worked with George Pinkerton, thought to be one of James' younger sons.
Work started in 1790 at the Ipswich end of the navigation, but there were problems. Baynes was sacked after less than a month, because of "unaccommodating and improper behaviour", and in November, Dyson and Pinkerton were dismissed for trespassing on land which did not belong to the Trustees. Legal action followed, which caused delays and involved the Trustees in extra costs, although some work carried on during the lawsuit.
Smith set up a brickworks in January 1791, and a contract to build six locks was awarded to Samual Wright of Ipswich in June. Because of the dispute, the Ipswich end was not sufficiently completed to enable materials to be carried up the navigation, and so they had to be carried overland to enable work on the Stowmarket end to continue.
A verdict was reached in the dispute between Dyson and Pinkerton and the Trustees on 14 November 1791, but the outcome is unclear.
The Trustees next asked the civil engineer John Rennie (the elder) to assess the state of the project. His inspection was carried out in the presence of the Trustees on 13–15 December 1791, and he produced a report within a week. He reported that the section from Stowmarket and Needham Market, the other main town on the waterway, was almost complete, but advised that the tow-path would need to be raised in places. There were three turf and timber locks, but he suggested that further locks should be made of brick. He felt that while Jessop had laid out the plans prior to the obtaining of the initial Act of Parliament, there had been a failure to adequately survey the river and detail the works that would be required to construct the navigation. He particularly criticised Lenny's lack of accuracy, and recommended that a new survey should be made, so that the work needed could be identified.
He made his next report to the Trustees on 23 April 1792. He estimated that £12,762 would be required to finish the work, of which £6,600 would be needed for the remaining 12 locks, which he thought could be built for £550 each. He then inspected the lower river, and agreed that Jessop's original site for the junction between the navigation and the River Orwell was the best available. He suggested that the timber locks should be rebuilt, once the navigation began to make a profit, and recommended that another Act of Parliament should be obtained, to raise more money.
The Act was obtained on 28 March 1793, which authorised the Trustees to borrow an extra £15,000, as the original capital had all been spent. The final cost of construction was £26,263, which was nearly double the original estimate. The waterway was just under 17 miles long from Ipswich to Stowmarket, rising 90 feet through 15 locks of broad construction each 55 by 14 feet, suitable for barges with a draught of 3.3 feet.
It was opened throughout on 14 September 1793.