Thomas Johnson was one of the leading citizens of Liverpool, which he represented as a Whig for over 20 years, the last ten without opposition. A shipper and tobacco merchant, he was also a pioneer of the new rock salt industry, acting as its mouthpiece in Parliament. In 1711 he introduced a bill for making the river Weaver navigable from the Mersey to the rock salt works in Cheshire, which was rejected owing to the opposition of the brine salt and other interests but ultimately passed in 1721. He was largely responsible for providing Liverpool with a floating dock, engaging Thomas Steers to draw up plans and introducing a bill for the construction of the dock, which received the royal assent in 1710. Other municipal improvements and developments to which he contributed were the constitution of Liverpool as a separate parish, distinct from Walton; the building of St. Peter’s and St. George’s churches; and the establishment of the market in Derby Street. He was knighted on 20 March 1708, when he presented a loyal address from Liverpool on a threatened Jacobite invasion.After the accession of George I, Johnson supported the Government. In 1716, when some of the Jacobite prisoners taken at Preston pleaded guilty and begged for transportation, he submitted proposals to the Treasury for transporting them at 40s. per head, the prisoners to serve Johnson or his assigns for seven years. The offer was accepted, and in March the Treasury paid Johnson £1,000 in part payment of his contract. When some of the better class prisoners argued that they had pleaded for simple transportation and would not ‘consent to be slaves’, Johnson had them ‘turned into a dungeon ... and fed only with bread and water’. In the end, all the prisoners, numbering 639, were transported by Johnson. In 1717 he made an unsuccessful bid of £61,000 for the whole of the French part of St. Kitts in the West Indies, which had been advertised for sale by the commissioners for trade and plantations.
Johnson was frequently in financial difficulties over the redemption of the bonds which tobacco importers were allowed to deposit as security for the duty payable on tobacco stored in customs warehouses if not re-exported. In 1717 he and his partner and son-in-law, Richard Gildart, were in debt to the Crown in respect of unpaid duty on tobacco to the extent of £7,825 3s. 1d. On 18 January 1719 the collector of the customs at Liverpool reported to the commissioners of customs at London: "Sir Thomas Johnson and Mr. Richard Gildart are both in London raising money to pay off their debts to the Crown. But neither has yet paid any of the old bonds for long due but have sent ships and effects to London to raise money there for there is a great scarcity of it here and trading almost at a stand."
At the general election of 1722, his property qualification was called into question by his opponent. In 1723 he resigned his seat to take up the post of collector of customs on the Rappahannock River in Virginia, leaving Gildart to cope with his debts. He seems to have remained in Virginia until 1725, when he was given a pension of £350 p.a. in lieu of his office. He died in London at his lodgings in Charing Cross on 28 December 1728.
He is reputed to have been part owner of several slave ships operating out of Liverpool, including the first known ship in 1699. Sir Thomas married twice, first to Lidia Holt, who died in 1696 (buried 9 September), and then to Elizabeth Barrow. He was the father of Elizabeth Johnson (1689 – 1717), first wife of Alderman Richard Kelsall (1685 – 1749), Mayor of Liverpool 1717-1718.