Both can be used as nouns and verbs. Flounder is actually a type of fish. Your question is probably about the difference as verbs. Struggle, you probably know, is trying to do something, but having difficulty with it. The word implies some chance of success. Flounder implies that you may have been struggling, but things have taken a downturn and you are now in the process of failing--- but you are still alive. If you were swimming, then flounder would mean you are about to drown.