In December 1801, when Clairmont was three years old, her mother married a neighbour, the writer and philosopher William Godwin. This brought her two stepsisters: Godwin's daughter, later Mary Shelley, only eight months her senior, and his stepdaughter Fanny Imlay, a couple of years older. Both were the daughters of Mary Wollstonecraft, who had died four years before, but whose presence continued to be felt in the household. The new couple soon became the parents of a son, which completed the family.
Mary Jane and William married on 21 December 1801; this marriage, like his first, was precipitated by the bride's pregnancy. She gave birth six months later to a son they named William, but the infant died. She conceived again soon afterwards, and went on to have another boy, to whom they gave the same name: William Godwin the Younger, born in 1803.
Despite financial difficulties and a general dislike of Mary Jane among Godwin's friends, their marriage appears to have been solid, with Claire Clairmont describing her mother's 'affection and devotion to Godwin' as 'admirable and... unalterable from the day of their marriage till his death'. Her stepdaughter Mary wrote variously about Mary Jane: once writing that 'somthing [sic] very analogous to disgust arises whenever I mention her', but later - after her death - that 'It seemed strange that so restless a spirit could be hushed, & all that remained pent up in a grave. I had done all I could to help her during life'. The diarist Henry Crabb Robinson observed her to be "a meretorious wife".
Mary Jane and William remained married for 35 years, until Godwin's death in 1836. For some years they lived in grace and favour accommodation within the Palace of Westminster, following his award of a sinecure position as Office Keeper and Yeoman Usher of the Receipt of the Exchequer.