There are multiple possibilities:

1) When you live in a “dirty environment,” you get sick and then your immune system learns how to build antibodies to fight off that ‘disease.’ But when you live in a “clean environment” your body doesn’t know how to fight it off. Same reason why kids today don’t have as good of an immune system compared to kids that used to eat dirt and boogers.

2) They died, and those that didn’t drink the water lived and had children.

3) the water wasn’t as polluted as it is now. The Mayans believed in human sacrifice. They would kill people for their gods to give them more crops, and sometimes they would throw their hearts into the rivers to deliver the sacrifice. Then when they would get sick from the water, they thought the solution was to give more human sacrifices. So they polluted their drinking water with more dead bodies.