When you are in a sailboat, and you start getting gusts and choppy water, how do you describe what's happening to your boat? Can you say that it starts to "flounder," or is there a better word?
I think you are better off describing the conditions. Like choppy and or gusty.
The boat could heel / lean, rock, or even capsize.
It is more the captain and crew that are floundering.
Past flounder is distress. Crew and or boat need help.
I grew up around sailboats and live on an island. I have always heard the word "foundering" used to describe a boat taking on water and sinking. I have heard the word "flounder" used in connection with boats in less serious trouble.
A discussion of the usages can be found in Merriam-Webster:
When something founders, it loses its foundation. (Founder and foundation have the same root.) To founder is to collapse, sink, or fail. One source of confusion here is that the meaning of the verb flounder is similar: to flounder is to struggle to move or get one's footing, or to proceed or act clumsily or ineffectually. People can flounder, but ships founder.
A more "colloquial" discussion of the difference can be found here:
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.
The question also got some attention in the English Language & Usage stack,
If you gets gusts and choppy water, that's what we call "sailing". It happens. :)
If the gusts get severe, you reef the sails, or drop the sails altogether. Note that this is still within the normal parameters of sailing. Any competent sailor should be able to deal with this, until you get to gusts so severe that a person would have problems standing upright in the wind, until something breaks, or until your boat ends up somewhere dangerous (such as a lee shore).
If the boat starts to take on water and sink though, the word is founder. You were nearly there!
Mayday is a radio code indicating that you are in immediate lifethreatening danger. Pan-pan is a similar code indicating that there is an emergency but you are not in immediate danger. Neither is something you'd use as a word to describe the situation.
What are you actually looking for though? If you're trying to throw words at a piece of writing to make it sound authentic, I strongly suggest you don't. Unless you know what you're talking about, you're almost guaranteed to write something ridiculous, and there are enough people with basic knowledge of sailing to call you on it. If you particularly need expert guidance on how to make it sound authentic, write normally without using jargon, and then call in a friendly expert to advise you on turning it into something which actually works.
Not sure if this is a nautical term, and sure this won't be your favorite, but I have always heard the term "flagging" to indicate that someone or something has lost thrust or energy. If the forward progress of your sailboat slows down due to lack of wind, sail, or other means of propulsion, as in hitting a head wind or choppy seas, you and/or your boat could be said to be "flagging".