1590s, perhaps an alteration of founder (q.v.), influenced by Dutch flodderen "to flop about," or native verbs in fl- expressing clumsy motion. Figurative use is from 1680s. Related: Floundered; floundering. As a noun derived from this sense, from 1867.
flatfish, c.1300, from Anglo-French floundre, from Old North French flondre, from Old Norse flydhra; related to Middle Low German vlundere, Danish flynder; ultimately cognate with Greek platys "flat, wide, broad" (see plaice (n.)).