The 1674 first edition of The Compleat Gamester is attributed to Cotton (by publishers of later editions, to which additional, post-Cotton material was added in 1709 and 1725, along with some updates to the rules Cotton had described earlier. The book was considered the "standard" English-language reference work on the playing of games – especially gambling games, and including billiards, card games, dice, horse racing and cock fighting, among others – until the publication of Edmond Hoyle's Mr. Hoyle's Games Complete in 1750, which outsold Cotton's then-obsolete work.[2]

At Cotton's death in 1687 he was insolvent and left his estates to his creditors. He was buried in St James's Church, Piccadilly, on February 16, 1687.

Cotton's reputation as a burlesque writer may account for the neglect with which the rest of his poems have been treated. Their excellence was not, however, overlooked by good critics. Coleridge praises the purity and unaffectedness of his style in Biographia Literaria, and Wordsworth (Preface, 1815) gave a copious quotation from the "Ode to Winter". The "Retirement" is printed by Walton in the second part of the Compleat Angler.

He was a Derbyshire man: his father moved there from the South England to live on his wife's estates. The Peak district is no longer associated with trout fishing. In Cotton's day, the inaccessibility of good fishing spots was physical as well as legal. The opening chapters of his section of the Compleat Angler draw Cotton and his friend across a savage and mountainous landscape. The friend, who will be taught fly-fishing, expresses doubt as to whether they are still in Christendom.