Just before the War of 1812, Calvin Cook purchased the mill and, together with his brother Noah, eventually adding a tannery, a sawmill and a distillery.

Toward the end of the War of 1812, a fire fight occurred at Cooks Mills, involving an American contingent sent to destroy flour and grain that might benefit the British.

On the morning of October 19, 1814, the American picket just east of the mills was attacked by soldiers of the Glengarry Light Infantry and other British regiments.

The remains of American and British soldiers killed in the battle lie buried in unmarked graves near the creek.

Eventually, the flow in Lyons Creek decreased to the extent when it was no longer able to turn the water wheels at Cooks Mills.

Over time, the apostrophes indicating the possessive in Lyon's Creek and Cook's Mills were dropped following a trend in the region exemplified by St. Catharines and St. Johns West.

The Ontario Ministry of the Environment is investigating the source of PCBs and possible remedial actions to deal with contaminated sediment.