It speeds up transit time. Caffeine-containing beverages can affect your digestive system and cause diarrhea, especially if you have a condition that affects your bowels, such as irritable bowel syndrome. 2. It’s a diuretic. That means caffeine makes your body lose water. This could potentially set the stage for dehydration and put you at risk for constipation. Without enough liquid or fluid in the colon, stool can become hard and have a more difficult time traveling through your digestive system.