He was the second son of Louis I, Prince of Anhalt-Köthen, but second-born son of his second wife Countess Sophie of Lippe, daughter of Simon VI, Count of Lippe.
William Louis was only twelve years of age when he succeeded his father in Köthen in 1650.
During his minor years, his uncle Prince Augustus of Anhalt-Plötzkau acted as regent.
After the death of Augustus in 1653, his sons Lebrecht and Emmanuel took over the regency until William was formally proclaimed of age in 1659.
In Köthen on 25 August 1663 William Louis married Elisabeth Charlotte (b. Harzgerode, 11 February 1647 - d. Osterholm, 20 January 1723), daughter of his cousin Frederick, Prince of Anhalt-Harzgerode, and granddaughter of Christian I, Prince of Anhalt-Bernburg.