For quite some time, I’d assumed that I simply didn’t understand these two words. I’ve seen the verb “to founder” in print, quite often where I expected “to flounder.” As such, I decided that flounder probably wasn’t proper English, but rather a perversion of the real word, “to founder.”
I even went so far as to inform people of my error in this matter. None of them thought (or knew) to correct me, so I proceeded to think that I had solved the mystery.
It wasn’t until recently that I finally got around to investigating the difference, and was surprised by what I found.
First, both founder and flounder are real English verbs. And indeed they are used in roughly the same context, though they do mean different things.
This usage guide, from the American Heritage Book of English Usage, is perhaps the best and most simple explanation I can find:
People often confuse the verbs founder and flounder. Founder comes from a Latin word meaning “bottom” (as in foundation) and originally referred to knocking enemies down; people now use it also to mean “to fail utterly, collapse”: The business started well but foundered. Flounder means “to move clumsily, thrash about” and hence “to proceed in confusion.” Thus if John is foundering in Chemistry 1, he had better drop the course; if he is floundering, he may yet pull through.
Thus, I floundered with this distinction. But, by looking it up, I saved myself from foundering. And that’s good to know.