The couple had two sons and seven daughters. The eldest daughter, Gertrude, married Sandford Hall Fleming, eldest son of Sir Sandford Fleming, the inventor of Standard Time, while another daughter, Marion, divorced wife of Alfred Louis Castellain, became, secretly, in 1906, the wife of Sir Frederick W. A. G. Haultain, the man her father had appointed as first premier of the Northwest Territories in 1897. Of the sons: the elder, Edward Compton Mackintosh, died of a fever, on 28 January 1901, at Pretoria, while he was serving as a private in the Canadian contingent with Lord Strathcona's Horse fighting in the Second Boer War. The younger, Charles St Lawrence Mackintosh, who had served as his father's personal secretary and aide-de-camp when he was N.W.T. lieutenant governor, first married Eileen White of Quebec City, granddaughter of Sir Hugh Allan, in 1899. They had a son, Charles Allan Mackintosh, born in 1901. Divorced in 1906, he remarried, in 1908, to Kate Totten Putnam (d.1919), and was married for the last time, in 1927, to Lillie Tupper Cameron, whose mother was the eldest child of Canadian Conservative Prime Minister Sir Charles Tupper, 1st Baronet.