On 29 October 1663, he married firstly Catherine Primrose, daughter of Sir Archibald Primrose, 1st Baronet and had by her five sons and five daughters.[4] She died in 1677, and Carnegie married next Catherine Gordon, daughter of Robert Gordon and widow of Robert Arbuthnot, 2nd Viscount of Arbuthnott, on 29 October 1684.[4] His second wife bore an only son and died in 1692.[4] Carnegie married finally Jean Burnett, daughter of James Burnett about 1696, and had by her three sons and three daughters.[4] He died in 1708 and was succeeded in the baronetcy by his oldest son John.[2]