The volumes of coal transported along the canal were lower than had been predicted, hampered by the lack of a proper link from Coalisland to the collieries, but trade in flaxseed, grain, rock salt, timber, fish and coarse hardware gradually built up. However, its condition deteriorated, and by 1801, it was almost derelict. Control of inland waterways was returned to central government, and the Directors General of Inland Waterways send an engineer called Henry Walker to inspect it. He began work on repairing the canal, but was dismissed and replaced by John Brownrigg in September 1801, as similar work he had carried out on the Newry Canal was alleged to be defective. Brownrigg reported that much of the canal was dangerous, and a third opinion was sought from the engineer Daniel Monks. Between 1801 and 1812, over £20,000 was spent on the canal, which included scouring the basin at Coalisland, building wharves, stores and boundary walls around it, rebuilding of lock walls and floors, dredging the whole canal to give a depth of , repairs to lock houses, puddling of the lower reaches where it passed through peat, and upgrading of the towpaths.