The species is known from fossil seeds and fruits found in the early Eocene Okanagan Highlands deposits of northern Washington state and British Columbia, Canada.

Nuphar carlquistii fossils have been identified from two locations in Western North America, the 49 million year old Klondike Mountain Formation near Republic, Washington and at the Thomas Ranch locality near Princeton, British Columbia.

[3] The specimens were studied by paleobotanists Melanie DeVore, Witt Taylor, and Kathleen Pigg with the type description for N. carlquistii being published in a 2015 International Journal of Plant Sciences article.

[1] In the type description, the species name was applied to fruits and seeds specifically, while fossils of associated but not attached tepals, stigmatic disks and rhizome sections were discussed as Nuphar cf carlquistii.

One of the rhizome segments, UWBM 57225A showing root attachment points, had previously been published with an informal identification as banana fruit of the genus Ensete.