Sir John Lowther, 2nd Baronet FRS (9 November 1642 – 17 January 1706) was an English gentleman and landowner at Whitehaven.
Lowther was born at Whitehaven, St Bees, Cumberland, the son of Sir Christopher Lowther, 1st Baronet, and his wife, Frances Lancaster, daughter of Christopher Lancaster of Stockbridge, Westmoreland. He was educated at Ilkley, Yorkshire and Balliol College, Oxford (matriculated 1657) Lowther owned large coal estates near Whitehaven, and worked to develop the mines and the port. He spent over £11,000 in expanding Lowther holdings in the Whitehaven area, concentrating on the acquisition of coal-bearing land, of land which would allow his pits unhampered access to Whitehaven harbour, and land which would hinder the working of others' pits. This, in turn, allowed him to improve the drainage of his pits, unworried by the thought that he was also draining his neighbours'. He secured the grant of the right to hold a market and a fair to Whitehaven, and its recognition as a separate customs 'member-port' (under the 'head-port' of Carlisle) responsible for the Solway coast from Ravenglass to Ellenfoot (later Maryport). He also secured (against a rival grant to the Earl of Carlingford), recognition of his title to the foreshore (land between low-water and high-water) of the manor of St. Bees, containing 'houses lands staythes & salt pans at Whitehaven' valued at £400 a year. He oversaw the rise of Whitehaven from a small fishing village (at his birth it consisted of some fifty houses and a population of about 250) to a planned town three times the size of Carlisle. At his death the 'port of Whitehaven' had 77 registered vessels, totaling about four thousand tons, and was exporting over 35,000 tons of coal a year.
He served as Member of Parliament for Cumberland from 1665 to 1701, and a Lord Commissioner of the Admiralty from 1689 to 1696.
Lowther died at Whitehaven and was buried at St Bees.
Lowther married Jane Leigh, a ward of his uncle Sir John Lowther of Lowther (because a daughter (by her first marriage to Woolley Leigh of Addington, Surrey) of Elizabeth Lowther (née Hare) who had taken as her second husband Sir John Lowther of Lowther). Lowther and Jane had three children: