If you’re going to get sick while traveling, it will probably be from contaminated water or food. As a tropical country, Ecuador is full of bacteria and parasites, and the Galápagos is no exception. Get in the habit of washing your hands at least 2-3 times a day, preferably before every meal and certainly after every restroom visit.
Hygiene is generally of a good standard on organized tours, and you’re more likely to get sick eating and drinking at cheap places in the ports. Even then, it’s less likely than on mainland Ecuador. Obviously, drink only bottled water and never from the faucet. This becomes more complicated when ordering drinks made with water. To minimize the risk, drink bottled fruit juices or sodas, which are readily available in port and on ships. However, you’re bound to want to try the freshly made juices and shakes, which can be a risk because they are occasionally mixed with unpurified water. You’ll be fine in reputable hotels, but avoid the cheaper joints. Ice cubes are a particular risk, so ask for drinks sin hielo (without ice).
No one is safe from traveler’s diarrhea, although most cases are mild. Ease a low-grade case of the runs with Imodium A-D (loperamide) or Pepto-Bismol, but bear in mind that these medicines are often short-term solutions. Drink plenty of water and noncaffeinated fluids like fruit juice and ginger ale. Oral rehydration solutions are very handy, and if you haven’t brought any, they’re easy to make: One teaspoon of salt and 2-3 tablespoons of sugar or honey in a liter of water will work. More serious cases may require a doctor’s appointment and antibiotics. Your guide may be able to recommend a good antibiotic for bacterial infection to get from the pharmacy.
Dengue fever, transmitted by Aedes mosquitoes, is present on the Galápagos, although it is rare. There have been outbreaks occasionally on San Cristóbal, but these are confined to urban areas because the mosquitoes live mainly in dirty water. Flu-like symptoms, such as nausea, bad headaches, joint pain, and sudden high fever are often misdiagnosed as other tropical diseases. Severe cases leading to shock syndrome or hemorrhagic fever are rare, but if you have already had dengue fever, a second case can be more dangerous. The only treatments known so far are rest, fluids, and fever-reducing medications. Medical attention is strongly recommended, if only for diagnosis.