The Hudson River Museum collects cultural, social and historical material related to the Museum's historic Mansion and the wider Westchester County/Hudson River Valley region. The Museum is also home to a modest collection of 19th- and 20th-century American art.

The Museum's collections have evolved from the original holdings of the Yonkers Museum, which was founded at City Hall in 1919, and relocated to the Yonkers Museum of Arts and Science in 1924. During it's early years, the Museum attempted to be much more global in its programmatic approach. Collection materials were placed on permanent display in galleries devoted to natural history, earth science, local and world history, and fine arts. In 1937, H. Armour Smith--an avid collector of fine art, Americana and documentary materials--became director. Smith advocated changing the Museum's name to The Hudson River Museum--to acknowledge that its collections documenting the Hudson River Valley were of primary importance to the Museum's goals. In 1956, the transfer of the stuffed elephant Tip, a popular display since 1929, to the Elephant Hotel in Somers, New York, was indicative of the changes that had occurred in the Museum's perception of its mission.

By 1948, when the Museum was rechartered by the New York State Board of Regents as The Hudson River Museum at Yonkers, Inc., the collection had grown to include a small group of 19th and 20th century fine arts--paintings, sculptures, and graphic works--as well as Victorian furniture, decorative arts and costumes, and materials documenting local history. In 1969, the New Wing added approximately 15,000 square feet of gallery space. Whereas previously much of the museum in the Mansion had been devoted to permanent displays, the new galleries were used for changing exhibitions of art, history and science. At the same time, the Mansion's first floor was partially restored, with four furnished period rooms and two small galleries for displaying decorative and historical materials from the collection.

In the late 1970s, Director Richard Koshalek proposed that the Museum, with little space to devote to storing and exhibiting contemporary art, could incorporate art of its time into the fabric of the new building. With funds from the National Endowment for the Arts and several foundations and corporations, the Museum commissioned two permanent installations. The first to be completed was Red Grooms' The Bookstore, a sculptural environment that would also function as the Museum' gift shop, followed by Dan Flavin's fluorescent light installation Untitled (for Betty and Richard Koshalek, a reminder), 1979.

Today, the Museum's collections reflect its mission to provide for development, preservation, and display of 19th- and 20th-century American art and history. The staff regularly organizes special collection exhibits and loan exhibits in which the permanent collections can play a role. Paintings, furniture and decorative arts are also always on view in the six period rooms in Glenview Mansion and its second floor hall and Lifflander Galleries.