To flounder is to struggle, but to founder is to sink like a stone and fail. Both are fun as nouns, not so fun as verbs.
A flounder is a fish, but as a verb, it means to blunder about, to be in serious trouble. In the following examples, something is struggling but hasn't completely failed:
He set out for it, limping, while the sharp gravel rolled under his bleeding feet as he floundered up the climbing trail. (Harold Bindloss)
It is a war that has floundered for nine years without a rational strategy and may endure for another decade. (Sydney Morning Herald)
Just as he turned around that floundering business, he suggests, so too could he reverse the country's sagging fortunes as its chief executive. (Washington Post)
A founder is someone who starts something, but as a verb, founder literally means "to sink." Figuratively, it's "to collapse or fail completely." Here are some examples of sinking and failing:
Pratt resisted the impulse of most Mormons to head back to the foundering ship. (Salt Lake Tribune)
Xinhua, in an English-language commentary, said China could not stand by while its largest trading partner foundered. (Reuters)
Yet negotiations over new gas contracts have foundered. (Economist)
Flounder and founder are happy little nouns that don't get mixed up. But it all falls apart when they're verbs — if you're floundering, you're struggling. If you're foundering, you're failing completely. You're sunk! You can't even hold onto the letter l.