He was named after his uncle Charles Emmanuel III of Sardinia, husband of his aunt Polyxena of Hesse-Rotenburg.
He was born in Langenschwalbach, the son of Constantine, Landgrave of Hesse-Rotenburg (24 May 1716 – 30 December 1778) and his first wife, Countess Maria Sophia Theresia Hedwigis Eva von Starhemberg (October 1722 – 12 December 1773), widow of William Hyacinth, Prince of Nassau-Siegen and sister of Georg Adam, Prince of Starhemberg.
Karl Emanuel married Princess Leopoldina Maria Anna Francisca de Paula Adelgunda of Liechtenstein (Vienna, 30 January 1754 – Frankfurt, 16 October 1823), daughter of Franz Josef I, Prince of Liechtenstein, on 1 September 1771 in Felsberg.
Karl also had an illegitimate son by Lucie Juliane Amalie Struve (b.
1769), daughter of Johann Conrad Struve (d. 1782), Quartermaster from Braunschweig: Karl's only descendants were from his illegitimate line.