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.
figurative sense is attested from 1832, from profit-and-loss accounting, where the final figure calculated is the bottom line on the page. Also (especially as an adjective) bottom-line, bottomline.
1670s, "a bottom, the bottom; foundation, groundwork," from French fond "a bottom, floor, ground" (12c.), also "a merchant's basic stock or capital," from Latin fundus "bottom, foundation, piece of land" (from PIE root *bhudh- "bottom, base," source also of Sanskrit budhnah, Greek pythmen "foundation, bottom," Old English botm "lowest part;" see bottom (n.)). Meaning "stock of money or wealth available for some purpose" is from 1690s; sense of "store of anything to be drawn upon" is from 1704. Funds "money at one's disposal" is from 1728.