Attempts began in the 16th century to improve the upper non-tidal section of the river for navigation. The river was improved in stages following a series of Acts of Parliament throughout the 18th century, with the navigation being completed to Northampton in 1761. The link to the Grand Junction Canal and the wider canal system was completed in 1815 via lock 17 of the Northampton Arm. However, the conditions of the navigation was not maintained and the coming of the railway to Northampton in 1845 reduced the navigation‘s profitability, which led to further deterioration of the river’s infrastructure.
The Nene Catchment Board took control of the river as result of the Land Drainage Act of 1930. The board rebuilt all the locks and replaced remaining staunches with sluice gates. There are a total of 38 locks which maintain water levels for navigation and also discharge floodwater in times of high flow. For this reason, most of the Nene locks have upstream pointing doors and substantial guillotine gates. This unique design is an important heritage aspect of the navigable river. The Environment Agency has been the navigation authority for the River Nene since 1996. The Nene forms an important link between the main waterways network of the Midlands and the South via the Northampton Arm of the Grand Union Canal through to the Fens waterways using the Nene-Great Ouse Navigation Link. This leaves the main Nene navigation channel at Stanground Lock on the South Eastern edge of Peterborough and follows the old course of the Nene on the Middle Level Navigations.
As profits dwindled on canals, companies were bought up. The Grand Junction Canal merged with other canals in 1929 to become the Grand Union Canal (as it is known today). By 1970, there was no long-distance transport on the canal.
The first recorded attempts to improve the upper river for navigation occurred in 1567 and 1606, when the people of Northampton commissioned surveys. In 1653, a printed pamphlet suggested that 33 locks to bypass the mills could be built for £8,000, to make the river navigable. Eventually, an Act of Parliament was obtained in 1713, which appointed large numbers of Commissioners, but stated that work could only proceed if any nine of them could find someone to make the entire river navigable. No-one was prepared to take on the task, although it appears from the Act that the river was navigable from Peterborough to Alwalton at the time. The Act was superseded by a second one obtained in 1724, which allowed the river to be improved in stages, the work to be carried out at the contractor's expense, with the cost to be recouped from tolls. Robert Wright and Thomas Squire agreed to these terms for the section from Peterborough to the bridge at Oundle North in September 1726, and completed the work by 1730. Squire then agreed to the same terms for the next section to Thrapston in 1736, and completed it by late 1737. This part of the river was then designated as the Eastern Division.
A failure to find anyone prepared to work on the Western Division from Thrapston to Northampton resulted in a third Act being obtained in 1756, which allowed the Commissioners to borrow money to finance the work. Lenders would become Proprietors of the Navigation, and the work was to begin at Thrapston and extend the navigable section towards Northampton. It took the Commissioners two years to agree who should carry out the work, but on 22 June 1758, John Smith jnr from Attercliffe, Yorkshire was contracted to construct 20 pound locks, 20 horse haling bridges and various other works at a cost of £14,070. The river opened to navigation in stages over the next three years, with a great celebration being held at Northampton on 7 August 1761 when the work was completed.
The proprietors had the right to use tolls as they saw fit, and the Commissioners found that they had no powers to ensure the navigation was maintained in good order. They obtained another Act of Parliament in 1794, which aimed to rectify the situation, but it was not until 1801 that Thomas Wright replied to their requests, and some repairs were made. There was little traffic and income from tolls was low, at just £488 per year between 1801 and 1804. The Commissioners were also keen to see a link constructed from Northampton to the Grand Junction Canal, but the canal company argued that there was an insufficient supply of water. It was agreed that a link would be built in two halves, but that there would be 1 mile (1.6 km) of railway in the middle. When built, the canal company constructed the entire link as a railway, which opened in 1805. In a bid to get a navigable link, the Commissioners opposed the bill to build a link between the Grand Junction Canal and the Old Union Canal, but relented when they had a firm agreement that a navigable link to Northampton would be built. The link cost £35,000, was supervised by Benjamin Bevan, and was built between 1812 and 1815. It was nearly 5 miles (8.0 km) long, and dropped 107 feet (33 m) through 17 locks.
Tolls rose to a little over £1,000 per year, but the Commissioners decided that the canal boats damaged the locks, and all traffic had to be transferred to river barges. This order was withdrawn in 1827, but the condition of the river gradually deteriorated, and the arrival of the Blisworth to Peterborough Railway in 1845 further reduced profitability. Flooding was also a problem, but the Commissioners had no powers to act as Commissioners of Sewers, to address the problems of drainage. With serious flooding in December 1848, a public meeting was held, and a committee was elected to consider Nene drainage. The main problem was a restriction at Wisbech, and the engineer James Rendel estimated that £120,000 was required to reconstruct the river below Peterborough. The Nene Valley Drainage and Improvement Act was obtained in 1852, to allow this work to be completed
There are canal locks at fairly regular intervals which will accommodate boats up to 78 by 13 feet (23.8 by 4.0 m), with a draught of 4 feet (1.2 m), although most of the boats on the upper river are canal-type narrowboats and river cruisers. Below Peterborough, boats are restricted by the size of Dog in a Doublet lock, which is 130 by 20 feet (39.6 by 6.1 m) with 6.7 feet (2.0 m) draught, while below Wisbech, small ships can be accommodated. All but a handful of the locks have conventional mitre gates at the upstream end and a single vertically lifting guillotine gate at the downstream end. This arrangement permits the use of the locks as additional weirs in time of flood, when the mitre gates are chained open and the guillotines lifted to allow the water to flow straight through. This precludes navigation at these times.
Traditionally the guillotines were manually operated by turning a large wheel some 150 times to raise or lower the gate; since the locks have to be left empty this operation will always have to be done twice to pass through. In recent years the Environment Agency, who are the navigation authority for the river, have been installing electric operation of the guillotines and in some cases replacing them altogether with mitre gates.