"hole, cavity," Old English pytt "water hole, well; pit, grave,"
from Proto-Germanic *puttjaz "pool, puddle" (source also of Old Frisian pet, Old Saxon putti, Old Norse pyttr, Middle Dutch putte, Dutch put, Old High German pfuzza, German Pfütze "pool, puddle"),
early borrowing from Latin puteus [2.] "well, pit, shaft," which is perhaps
from [1.] PIE root *pau- (2) "to cut, strike, stamp," but there are phonetic and sense objections, so perhaps a loan-word. Meaning "abode of evil spirits, hell" is attested from early 13c. Pit of the stomach (1650s) is from the slight depression there between the ribs.
Why did linguists impute 2 to 1? Wiktionnaire also asserts this semantic shift.