I've looked everywhere from guidebooks to the CDC website, but haven't been able to find out what is in the water in Mexico that makes it unhealthy to drink. I'm asking because my backpacking water filter takes care of bacteria and protozoa, but not viruses, and I'm wondering if that will cover me. We'll be backpacking around the Sian Ka'an Reserve in Quintana Roo.
You can probably look at Index Mundi as a starting point, which lists potential food and waterborne diseases like:
food or waterborne diseases acquired through eating or drinking on the local economy:
Hepatitis A - viral disease that interferes with the functioning of the liver; spread through consumption of food or water contaminated with fecal matter, principally in areas of poor sanitation; victims exhibit fever, jaundice, and diarrhea; 15% of victims will experience prolonged symptoms over 6-9 months; vaccine available.
Hepatitis E - water-borne viral disease that interferes with the functioning of the liver; most commonly spread through fecal contamination of drinking water; victims exhibit jaundice, fatigue, abdominal pain, and dark colored urine.
Typhoid fever - bacterial disease spread through contact with food or water contaminated by fecal matter or sewage; victims exhibit sustained high fevers; left untreated, mortality rates can reach 20%.
What else could potentially be in the water might depend on the region and industry such as potentially pesticides or other chemicals.
This came up in a microbio class I took in college. Apparently Giardia is a major player in the problem with Mexico's water. It is a parasite that is very easily spread, especially when water municipalities aren't up to par. I did a quick search for some more in depth info on Giardia so I didn't have to type it all out again. I would say your water filter should help as far as drinking water is concerned, but you also have to be careful about contaminated food, pools, other people, etc. http://www.mayoclinic.org/diseases-conditions/giardia-infection/basics/definition/CON-20024686