In 1869, he married Lady Anne Noel, who was the daughter of the Earl of Lovelace and granddaughter of Lord Byron. Together they travelled through Spain, Algeria, Egypt, the Syrian Desert, and extensively in the Middle East and India. Based upon pure-blooded Arabian horses they obtained in Egypt and the Nejd, they co-founded Crabbet Arabian Stud, and later purchased a property near Cairo, named Sheykh Obeyd which housed their horse breeding operation in Egypt.

In 1882 he championed the cause of Urabi Pasha, which led him to be banned from entering Egypt for four years. Blunt generally opposed British imperialism as a matter of philosophy, and his support for Irish causes led to his imprisonment in 1888.

Wilfrid and Lady Anne's only child to live to maturity was Judith Blunt-Lytton, 16th Baroness Wentworth, later known as Lady Wentworth. As an adult, she was married in Cairo but moved permanently to the Crabbet Park Estate in 1904.

Wilfrid had a number of mistresses, among them a long term relationship with the courtesan Catherine "Skittles" Walters, and eventually moved another mistress, Dorothy Carleton, into his home, an event which triggered Lady Anne's legal separation from him in 1906. At that time, Lady Anne signed a Deed of Partition drawn up by Wilfrid. Under its terms, unfavorable to Lady Anne, she kept the Crabbet Park property (where their daughter Judith lived) and half the horses, while Blunt took Caxtons Farm, also known as Newbuildings, and the rest of the stock. Always struggling with financial concerns and chemical dependency issues, Wilfrid sold off numerous horses in order to pay debts, and constantly attempted to obtain additional assets. Lady Anne left the management of her properties to Judith, and spent many months of every year in Egypt at the Sheykh Obeyd estate, moving there permanently in 1915.

Due primarily to the manoeuvring of Wilfrid in an attempt to disinherit Judith and obtain the entire Crabbet property for himself, Judith and her mother were estranged at the time of Lady Anne's death in 1917, and thus Lady Anne's share of the Crabbet Stud passed to Judith's daughters, under the oversight of an independent trustee. Wilfrid filed a lawsuit soon afterward. Ownership of the Arabian horses went back and forth between the estates of father and daughter in the following years. Wilfrid sold yet more horses in his control, mostly to pay off debts, and shot at least four in an attempt to spite his daughter, action which required intervention of the trustee of the estate with a court injunction to prevent him from further "dissipating the assets" of the estate. The lawsuit was eventually settled in favour of the granddaughters in 1920, and Judith bought their share from the trustee, combining it with her own assets and reuniting the stud. Father and daughter briefly reconciled shortly before Wilfrid's death in 1922, but his promise to rewrite his will to restore Judith's inheritance never materialised.