John Mercer married Mary Wolstenholme in 1814.

They had six children, although the eldest only lived for 16 days.

Their second daughter, also Mary, died at the age of 19 years, much to her father's distress. 

She had shown great promise as a scientist and it is much to her father's credit that he should have given her such encouragement as he did. He felt her loss keenly. 

His sons followed him into the chemistry business, and all children remained unmarried.

His daughter Maria died aged 93 in 1913, leaving money to provide for lasting memorials to her father.