From its opening in 1900, the Marianna campus sprawled across roughly 1,400 acres without any perimeter fencing -- an open campus in name, a closed world in practice. The site was divided into two sub-campuses: the South Side, called "Number 1," for white students, and the North Side, "Number 2," for Black students. The sections remained segregated until 1966. Children committed for offenses ranging from theft and truancy to "incorrigibility" -- and some who were simply orphaned or abandoned when no other placement could be found -- lived under conditions the state investigated six times in the school's first thirteen years alone. A 1914 dormitory fire killed an estimated six to ten students and two staff members. Eleven students died in the 1918 Spanish flu epidemic, unnamed, ranging in age from ten to sixteen.

The worst abuses centered on the small building where corporal punishment was administered. Former students who endured the 1950s and 1960s -- a group that would later call themselves the White House Boys -- described being whipped until they blacked out, with punishments intensified for those who cried. Staff used leather straps, having switched from wooden paddles out of concern the paddles might cause injury. One former student reported receiving more than 250 lashes across eleven visits. Others alleged the existence of a "rape room" where guards sexually abused boys. Corporal punishment at the school was officially banned in August 1968. The White House itself was closed in 1967. But the culture of violence did not end with the building's closure; allegations of abuse continued through every subsequent decade until the school finally shut down.

A cemetery on the North Side, known as Boot Hill, held 31 simple crosses installed in the 1960s and 1990s -- markers that investigators later found did not correspond to specific burials. In 2012, forensic anthropologist Erin Kimmerle of the University of South Florida began excavating the site. Her team found remains of 55 bodies, almost twice the number documented in official records. Only 13 were buried within the cemetery grounds. The rest lay outside -- in the woods, under a roadway, beneath brush, under a large mulberry tree. By the time Kimmerle issued her final report in January 2016, the team had made seven DNA matches and 14 presumptive identifications. Three times as many Black students as white students had died and been buried at Dozier. In 2019, ground-penetrating radar identified an additional 27 suspected graves during preliminary work for a pollution cleanup.

Governor Charlie Crist ordered the Florida Department of Law Enforcement to investigate in December 2008, following public pressure from the White House Boys and their advocates. The 15-month FDLE investigation conducted more than 100 interviews but found no concrete evidence linking student deaths to staff actions. A forensic examination of the White House building detected no trace evidence of blood. The Department of Justice investigation in 2011 was more damning, citing staff for excessive force, inappropriate isolation, and extended confinement. The school closed permanently on June 30, 2011. On April 26, 2017, the state held a formal ceremony to apologize to two dozen survivors and families of victims. In 2024, a compensation bill carried by Representative Michelle Salzman and Senator Darryl Rouson was signed into law. The story entered American literature through Colson Whitehead's Pulitzer Prize-winning novel The Nickel Boys and its 2024 film adaptation.