I smell fish when you open your mouth. Did you brush your teeth after having breakfast? この表現は自然ですか？

It sound natural, but I would rephrase it since it can come off rude. Instead you could say, "your breath seems kind of fishy. Did you brush your teeth this morning?" People can still be offended by this, so a more polite way is to just say it as "something smells a bit fishy. Do you smell that?" So it won't be directed towards them, but it's a subtle hint. Or you can be even more modest (if you have either mints or gum), just take it out, take one for yourself, and also offer them one, so just be like "did you want a piece of gum?" Or "would you like a mint?"