Known as "turista", "traveler's sickness", and other names, for those who are not used to the microorganisms in the Central American water, don't be surprised if you become ill during your trip. We tried to be very careful to only drink factory-sealed bottled purified water ("agua purificada") wherever we went, but we both still came down with the stomach illness after only a few days in country. Fortunately we were prepared for it, because we had both visited a travel doctor in the U.S. prior to leaving to get our shots, our prescriptions for the anti-malarial pills (probably not necessary, but better safe than sorry), and an antibiotic prescription to combat the anticipated turista. We also bought some generic anti-diarrhea pills (to handle the most common symptom). When we did become ill we took the antibiotics and were back on track within a day. While the illness did weaken us and make for some minor inconveniences, it didn't keep us from keeping to our site schedule. Besides, I wasn't going to let an intestinal illness keep me off of any pyramids!
Here's my suggestions on this subject: 1) get an antibiotic from a travel doctor before you leave on your trip. 2) take anti-diarrhea medicine with you. 3) be careful what you drink or eat (certain drinks are made with the local water, certain foods are washed in it, etc.) You may want to stick with bottled drinks. Don't eat fresh fruit you didn't peel yourself or that wasn't prepared in a refutable eatery. 4) Don't wash your mouth out with the local tap water after you brush your teeth. Basically, just use your common sense and best judgment, but be prepared to get sick anyway. A final note: most of the hotels in Cancún and our hotel in Palenque have their own water purification system on the hotel grounds, so the tap water is safe to drink. Ask for bottled water otherwise. Another tip: If you are driving through the countryside, buy your bottled water in town at a grocery store/market; the prices are much cheaper there than if you try to stock up at the hotel.