I've been coming to Sayulita for a while now and have only been sick once. And I attribute that to the FLU that I might have picked up stateside before I flew down. However, we did bring down a group of 8 friends for New Years 2016 and just about all of them spent the better part of their vacation in the house sick. I think that its probably a combination of everything that everyone here has been talking about:
- The "polluted" river flowing into the ocean that everyone is surfing in
- Overpopulation in a very small place
- Poor food preparation and disposal
- Animals defecating in the streets
- People's immune systems failing due to excess booze, lack of hydration, sleep, etc.
So all that being said, its nice to see that the town locals are working on resolving the water treatment issues and have already tackled the river crossing concern. But in the end, this is a small village in Mexico and will never be a suburban town in Orange County where everything is sterile and clean. That would take away from the place itself.
Like SayuSoul said, if you want to stay healthy when down here, take care of yourself and don't do anything stupid. The longer you stay, the better you will be because your body will acclimate to the bacteria, etc. And like I always tell my daughter: hydration and sleep are your friends. The more you get, the healthier you will be.