There was, however, a method of punishment that was not officially sanctioned but was nonetheless permitted. When younger boys were deemed to have broken the Groton code -- by cheating, for example -- or were considered too "fresh," physical punishment was inflicted. There were two ways of doing so: the less severe, "boot boxing," consisted of being put into a basement locker assigned to each boy for the boots he wore outdoors. While in the box, the culprit would be painfully doubled up for as long a time as he was forced to remain in his tiny prison.-- James Chace, Acheson: The Secretary of State Who Created the American World (1998), at 23.
The second and more terrifying punishment was "pumping." This consisted of having one's face shoved under an open spigot in the lavatory for as long as it took to induce a sensation of drowning. If a boy was consistently out of line, two or three pumpings usually sufficed to curb any outward expression of his rebellion.
... Chace's source is a 1939 Harper's article by George Biddle. Googling "waterboarding Groton" produces other attestations:
The miscreant was bent back over the edge of a trough in the laboratory, face up, and water was poured in his face from an open spigot to simulate drowning. There was a 10-second limit to the torture, but it could be conducted more than once on any given occasion.The italicized passage is quoted from an article in American Heritage (see the previous link). See here for similar testimony in a biography of Col. Robert McCormick, of Chicago Tribune notoreity. Wiki places McCormick at Groton from 1893-99, which scotches my incipient theory that practices from the Philippines counterinsurgency had migrated back to prep schools; perhaps the causation went in the opposite direction?...
Little Teddy Roosevelt, Jr., a few weeks before his father was inaugurated as Vice-President, was pumped for being “fresh and swell-headed.” Half-drowned but still spouting defiance after two immersions, he escaped being put under for a third time: the boys admired his pluck. Malcolm Peabody, the rector’s own son, was pumped because the older boys didn’t like his “tone.”
These punishments were certainly still occurring in 1905, and for some years after that.