On October 13, 1869, he married Flora Payne, daughter of Senator Henry B. Payne of Ohio and sister of Whitney's Yale classmate, Colonel Oliver Hazard Payne, later treasurer of the Standard Oil Company.
The Whitneys lived in the now lost Stevens Mansion at 2 West 57th Street where they commissioned Stanford White to renovate the interiors.
 They had five children:
Harry Payne Whitney (1872–1930), who married Gertrude Vanderbilt (1875–1942)
Pauline Payne Whitney (1874–1916), who married Almeric Hugh Paget, 1st Baron Queenborough (1861–1949)
William Payne Whitney (1876–1927), who married Helen Julia Hay (1875–1944)
Oliver Whitney (1878–1883), who died aged 5
Dorothy Payne Whitney (1887–1968), who first married Willard Dickerman Straight (1880–1918) and later married Leonard Knight Elmhirst (1893–1974)
Flora Payne Whitney died on February 5, 1893, at age fifty-two.
Two years later, William Whitney remarried to  Sibyl Randolph (née May), a widow of a Mr. Randolph.
He gave his home at 2 West 57th street to son Harry and his new bride Gertrude, and acquired for his new wife a residence at 871 Fifth Avenue at 68th Street in New York City, and commissioned McKim, Mead & White to do a $3.5 million renovation of the house.
  In 1898, she suffered a horse riding accident at their estate, Joye Cottage, in the Aiken Winter Colony in Aiken, South Carolina, in what is now known as Hitchcock Woods and died at age forty-one on May 6, 1899.

Whitney was a member of Ward McAllister's "Four Hundred" as well as the Patriarch Society until its dissolution in April 1897.
 On January 5, 1901, at his residence, 871 Fifth Avenue, Whitney gave a debutante ball for his niece, Helen Barney.

He remained active in street-railway affairs until the reorganization of the Metropolitan Street Railway Company in 1902.
At that time he retired from all personal identification with the company.

William Collins Whitney died on February 2, 1904, and was interred at Woodlawn Cemetery in The Bronx, New York.
At the time of his death he was one of the largest landowners in the eastern United States, worth approximately $23 million (1/993rd of US GNP).
On October 13, 1869, he married Flora Payne, daughter of Senator Henry B. Payne of Ohio and sister of Whitney's Yale classmate, Colonel Oliver Hazard Payne, later treasurer of the Standard Oil Company. The Whitneys lived in the now lost Stevens Mansion at 2 West 57th Street where they commissioned Stanford White to renovate the interiors.  They had five children:
Harry Payne Whitney (1872–1930), who married Gertrude Vanderbilt (1875–1942)
Pauline Payne Whitney (1874–1916), who married Almeric Hugh Paget, 1st Baron Queenborough (1861–1949)
William Payne Whitney (1876–1927), who married Helen Julia Hay (1875–1944)
Oliver Whitney (1878–1883), who died aged 5
Dorothy Payne Whitney (1887–1968), who first married Willard Dickerman Straight (1880–1918) and later married Leonard Knight Elmhirst (1893–1974)
Flora Payne Whitney died on February 5, 1893, at age fifty-two. Two years later, William Whitney remarried to  Sibyl Randolph (née May), a widow of a Mr. Randolph. He gave his home at 2 West 57th street to son Harry and his new bride Gertrude, and acquired for his new wife a residence at 871 Fifth Avenue at 68th Street in New York City, and commissioned McKim, Mead & White to do a $3.5 million renovation of the house.   In 1898, she suffered a horse riding accident at their estate, Joye Cottage, in the Aiken Winter Colony in Aiken, South Carolina, in what is now known as Hitchcock Woods and died at age forty-one on May 6, 1899.
Whitney was a member of Ward McAllister's "Four Hundred" as well as the Patriarch Society until its dissolution in April 1897.  On January 5, 1901, at his residence, 871 Fifth Avenue, Whitney gave a debutante ball for his niece, Helen Barney.
He remained active in street-railway affairs until the reorganization of the Metropolitan Street Railway Company in 1902. At that time he retired from all personal identification with the company.
William Collins Whitney died on February 2, 1904, and was interred at Woodlawn Cemetery in The Bronx, New York. At the time of his death he was one of the largest landowners in the eastern United States, worth approximately $23 million (1/993rd of US GNP).
William Collins Whitney