Old English botm, bodan "ground, soil, foundation, lowest or deepest part of anything," from Proto-Germanic *buthm- (source also of Old Frisian boden "soil," Old Norse botn, Dutch bodem, Old High German bodam, German Boden "ground, earth, soil"). This is perhaps from PIE root *bhudhno- "bottom" (source also of Sanskrit budhnah, Avestan buna- "bottom," Greek pythmen "foundation," Latin fundus "bottom, piece of land, farm," Old Irish bond "sole of the foot").
Meaning "fundamental character, essence" is from 1570s; to get to the bottom of some matter is from 1773. Meaning "posterior of a person" (the sitting part) is from 1794. Bottoms up as a call to finish one's drink is from 1875. Bottom dollar "the last dollar one has" is from 1857. To do or feel something from the bottom of (one's) heart is from 1540s. Bottom-feeder, originally of fishes, is from 1866.