To the best of my knowledge that isnt really accurate. For one, smallpox, the biggest recurring epidemic disease, is from rats. Bubonic plague is from fleas on rats drawn to cowfeed and other grains stored in large quantities. Chickenpox, cowpox etc also from livestock.

For another, the water in pre-1800s Europe was much more drinkable than is commonly assumed. You might get worms, but generally you dont see the massive outbreaks of dysentry until urban populations explode from the 1600s on. Generally pre1800s epidemics are a complex mixture of lack of nutrition and a disease transmitted from some animal, rather than just "people drank their own shit".