I assume you are referring to when one is drinking water and accidentally chokes on it. Essentially your mouth is connected to both your digestive system and your respiratory system via your esophagus and your trachea respectively. We all have a small flap that covers the trachea or wind pipe when we are swallowing food or drink and opens when are breathing. When water “goes down the wrong tube” it means for some reason you tried to breath in while you still had some water in your mouth, so the flap open and water tried to go into your wind pipe. Your cough reflects generally keeps this from happening but you still have a momentary choking sensation.
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