He was the only child of Emmanuel, Prince of Anhalt-Köthen by his wife Anna Eleonore, daughter of Henry Volrad, Count of Stolberg-Wernigerode.
After the death of the Dowager Princess and his formally proclamation as adult, Emmanuel Lebrecht sent for Gisela Agnes and they finally married in a secret ceremony in Nienburg on 22 May (30 September according other sources) 1692. They had six children:
The morganatic marriage of a Reformist prince with a Lutheran low-noble woman received vehements protest of the Reformer Church and the other agnates of the Anhalt principalities. Nevertless, Gisela Agnes was created Imperial Countess of Nienburg (German: Reichsgräfin von Nienburg) on 23 July 1694.
The agnates refused to accept the marriage as dynastically valid and Emmanuel Lebrecht sued them before the Reichshofrat for libel in 1696; but finally, by treaty of 28 June 1698, the Princes of Anhalt-Bernburg, Anhalt-Harzgerode, Anhalt-Zerbst and Anhalt-Dessau recognized the issue of the marriage as lawful heirs and all descendants as princes and princesses of Anhalt with all appertaining rights, without however creating any precedent against the prescriptions of the law of the House of Ascania. The Imperial confirmation of the treaty was granted on 12 March 1699.
On 3 August of that year Emmanuel Lebrecht assigned his wife the castle, city and bailiwick of Nienburg as dowage per life and made her tutrix and regent in case of minority of his successor, with the full approval of the agnates. In 1702, he made a testament in were was introduced the Primogenitur in Köthen; later, these originated a dispute between his two surviving sons Leopold and Augustus Louis. Emmanuel Lebrecht died two years later leaving an infant successor, Leopold, who reigned until 1715 under the regency of his mother.