1660s, "stream of water or air flowing beneath the surface or beneath another current," a hybrid formed from under + current (n.). The figurative sense of "suppressed or underlying character" is attested from 1817.
Old English under (prep.) "beneath, among, before, in the presence of, in subjection to, under the rule of, by means of," also, as an adverb, "beneath, below, underneath," expressing position with reference to that which is above, from Proto-Germanic *under- (source also of Old Frisian under, Dutch onder, Old High German untar, German unter, Old Norse undir, Gothic undar), from PIE *ndher- "under" (source also of Sanskrit adhah "below;" Avestan athara- "lower;" Latin infernus "lower," infra "below").
Productive as a prefix in Old English, as in German and Scandinavian (often forming words modeled on Latin ones in sub-). Notion of "inferior in rank, position, etc." was present in Old English. With reference to standards, "less than in age, price, value," etc., late 14c. As an adjective, "lower in position; lower in rank or degree" from 13c. Also used in Old English as a preposition meaning "between, among," as still in under these circumstances, etc. (though this may be an entirely separate root; see understand).
Under the weather "indisposed" is from 1810. Under the table is from 1913 in the sense of "very drunk," 1940s in sense of "illegal" (under-board "dishonest" is from c. 1600). To keep something under (one's) hat "secret" is from 1885; to have something under (one's) nose "in plain sight" is from 1540s; to speak under (one's) breath "in a low voice" is attested from 1832.
late 14c., curraunt, "that which runs or flows," from Old French corant (Modern French courant), from Old French corant (see current (adj.)). Meaning "a flowing," especially "portion of a large body of water or air moving in a certain direction," is from 1550s. Applied from 1747 to the flowing of electrical force through a conducting body (electricity formerly was regarded as a sort of fluid).
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Definitions of undercurrent from WordNet
a subdued emotional quality underlying an utterance; implicit meaning;