Founder is related to Latin fundus, meaning "bottom" or "base." When something "founders," it usually hits the bottom in one sense or another. When a ship founders, it sinks to the bottom of the sea, for example, and if your endeavor is foundering, it isn't doing well and is therefore headed downward.
Verb Her career foundered, and she moved from job to job for several years. trying to save a foundering career
Word History
Etymology
Noun (1)
Middle English foundour, borrowed from Anglo-French fundur, foundour, going back to Latin fundātor, from fundāre "to found entry 4" + -tor, agent suffix
Verb
Middle English fondrer "to fall to the ground, stumble, sink," borrowed from Anglo-French fundrer "to destroy," probably back-formation from enfondrer, esfondrer, affondrer "to sink, send to the bottom," prefixed forms based on Old French -fondrer, going back to Vulgar Latin *-fundorāre, verbal derivative of Late Latin fundor-, variant stem of Latin fundus "bottom, base" — more at bottom entry 1
Note: The simple verb fundrer (as opposed to prefixed forms) is marginally attested in Anglo-French, its senses partially merged with fondre going back to Latin fundere (see found entry 5), which in addition to its basic meanings "to pour, cast" had already in Classical Latin the extended meanings "to scatter, disperse, rout" and "to lay low, slay."