Kennewick Man was discovered by accident by two college students, Will Thomas and David Deacy, on July 28, 1996. They were at the Columbia River to watch a hydroplane race near Kennewick. Thomas was wading in about 50 cm (18 in) of water, about 3 m (10 ft) from shore, when his foot struck something hard and round. He pulled up a human skull. They stashed it in the bushes, waited for the race to finish, then found a plastic bucket and took the skull to a Kennewick police officer. The police returned with the students to the location. Further searching found more bones underwater and along the shore. The county coroner determined the skull was not modern, and it was given to archaeologist James Chatters, who over the course of ten visits to the site, assembled 350 bones and bone fragments creating a nearly complete articulated skeleton.

The cranium was fully intact including all of its teeth from the time of death. All major bones were found except the sternum and a few in the hands and feet. After further study, Chatters concluded it was "a male of late middle age (40–55 years), and tall (170 to 176 cm, 5′7″ to 5′9″), and was fairly muscular with a slender build". The Owsley team in 2005 reported he may have been as young as 38 at the time of death.

A small bone fragment submitted to the University of California, Riverside for radiocarbon dating estimated he lived between 9,300 and 9,600 years ago (8,400 uncalibrated "radiocarbon years"), and not the 19th century, as had originally been thought. Subsequent radiocarbon dating indicated a somewhat younger age of 8,900 to 9,000 years BP, and later 8,400 to 8,690 calibrated years Before Present.
Measurements of carbon, nitrogen, and oxygen isotope ratios in the bone collagen indicate that the man lived almost exclusively on a diet of marine mammals for the last 20 or so years of his life, and that the water he drank was glacial melt. The closest marine coastal environment where this water could have been found during his lifetime was in Alaska. That, combined with the location of the find, led to the conclusion that the individual led a highly mobile, water-borne lifestyle centered on the northern coast.
Chatters found a 79 mm (3.1 in) stone projectile lodged in his ilium (part of the pelvic bone). There was new bone growing around it indicating a painful but old wound. Chatters made a CT scan which determined the projectile was made from a siliceous gray stone with igneous (volcanic) origins. The projectile, leaf-shaped, long, and broad, with serrated edges, fit the description of a Cascade point, characteristic of the Cascade phase from 12,000 to 7,500 years BP.

Forensic anthropologist Douglas Owsley, who later led the scientific team that examined Kennewick Man's skeleton in 2005, discovered that the bones in Kennewick Man's arms were bent. Owsley theorized that this was the result of powerful muscles built up over the course of a lifetime of hunting and spearfishing. Kennewick Man was found to be right-handed, as the bones of the right arm are noticeably larger than the left.

Owsley also found that Kennewick Man had arthritis in his right elbow, both of his knees, and several vertebrae but not severe enough to be crippling. Kennewick Man had suffered some trauma in his lifetime, which was evident by a fractured rib that had healed, a depression fracture on his forehead, and a similar indentation on the left side of the head, and a spear jab that healed.
Chatters, who initially investigated the skeleton, early on concluded that the "presence of Caucasoid traits [and a] lack of definitive Native-American characteristics", as well as the apparent context of the skeleton as part of an early Paleo-American group led him to state that the body was "Caucasian" (an anthropological term not synonymous with "white" or "European").

Scientists attempted DNA analysis within a few years of discovery, but reported "available technology and protocols do not allow the analysis of ancient DNA from these remains" ie. multiple experts were unable to extract enough DNA for analysis.

Chatters …

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In October 1998, the remains were deposited at the Burke Museum at the University of Washington. The Burke Museum was the court-appointed neutral repository for the remains, and did not exhibit them. They were then still legally the property of the US Army Corps of Engineers, as they were found on land under its custody.

According to NAGPRA, if human remains are found on federal lands and their cultural affiliation to a Native American tribe can be established, the affiliated tribe may claim them. Two months after discovery in 1996, the Umatilla tribe requested custody of the remains so they could be reburied according to tribal tradition. It was contested by researchers who believed Kennewick Man was not affiliated with modern Indians. The Umatilla argued that their oral history goes back 10,000 years, and they had been present on the territory since the dawn of time. Native American tribes asserted that the claims that Kennewick Man was of non-Indian origin was an attempt to evade the law governing custodianship of ancient bones. The Corps of Engineers and the Clinton administration supported the Native American claim in what became a long-running lawsuit.

Robson Bonnichsen and seven other anthropologists sued the United States for the right to conduct research. The anthropologists won the case in 2002, and on February 4, 2004, the United States Court of Appeals for the Ninth Circuit panel rejected an appeal brought by the United States Army Corps of Engineers and the Umatilla, Colville, Yakama, Nez Perce, and other tribes on the grounds that they were unable to show sufficient evidence of kinship. Furthermore, the presiding judge found that the US government had acted in bad faith and awarded attorney's fees of $2,379,000 to the plaintiffs.

On April 7, 2005, during the 109th Congress, United States senator John McCain introduced an amendment to NAGPRA, which (section 108) would have changed the definition of "Native American" from being that which "is indigenous to the United States" to "is or was indigenous to the United States". However, the 109th Congress concluded without enacting the bill. By the bill's definition, Kennewick Man would have been classified as Native American regardless of whether any link to a contemporary tribe could be found.
In September 2016, in light of new DNA evidence associating Kennewick Man with modern day Native Americans, the 114th US House and Senate passed legislation to return the ancient bones to a coalition of Columbia Basin tribes. The coalition included the Confederated Tribes of the Colville Reservation, the Confederated Tribes and Bands of the Yakama Nation, the Nez Perce Tribe, the Confederated Tribes of the Umatilla Reservation, and the Wanapum Band of Priest Rapids.

The remains of Kennewick Man were cataloged and removed from the Burke Museum on February 17, 2017. The following day, more than 200 members of five Columbia Plateau tribes were present at a burial of the remains, according to their traditions, at an undisclosed location.