Cotton married firstly  (with c.£8,500) Lettice Crowley, daughter of Sir Ambrose Crowley of Greenwich on 24 May 1714.
She died in August 1718 and he married secondly Margaret Craggs, the daughter of James Craggs on 3 June 1724.
He was succeeded in the baronetcy by his only surviving son, John Hynde Cotton, child of his first wife.

They lived at Madingley Hall for 40 years during which time he transformed it from a panelled Tudor house into a Baroque building.
Cotton married firstly  (with c.£8,500) Lettice Crowley, daughter of Sir Ambrose Crowley of Greenwich on 24 May 1714. She died in August 1718 and he married secondly Margaret Craggs, the daughter of James Craggs on 3 June 1724. He was succeeded in the baronetcy by his only surviving son, John Hynde Cotton, child of his first wife.
They lived at Madingley Hall for 40 years during which time he transformed it from a panelled Tudor house into a Baroque building.
Sir John Hynde Cotton, 3rd Baronet