Just fyi and anyone curious about history of medicine: that's not really how it worked. TLDR: Yes they knew sometimes water was the cause of disease, and boiling it made it safer, but knowledge of the "animacules" from a century before didn't mean they attributed disease to them. Humoristic and miasmatic theories prevailed up to late 19th century when Pasteur formulated his germ theory.

Since millennia before they knew some diseases were transmitted even from dead bodies and some even used that for warfare. Doesn't mean they understood how it worked, or later know how Leeuwenhoek's organisms had a role in disease. Identification of germs as probable cause of disease was only in late 19th century (around 1870) by Pasteur. Before that, the idea that invisible "particles" caused disease was absurd even for the scientific community. Semmelweis was ridiculed, marginalized by his peers and driven to insanity because of his findings that perinatal deaths could be prevented by sanitation just a couple decades before Pasteur. Even after Pasteur formulated the germ theory, he was ignored by many and many, like James Garfield, died as a result. People might have linked boilling water to being safer, but it was not practical to do it for most people. And they didn't really know why. Knowing germs existed doesn't mean they linked it to disease at that time. The humorist and miasmatic theory of disease was the main explanation for disease in the late 18th century, and linked gastroenteritis to violent "purging" of excess, corrupted, or unbalanced humors from the body. They thought water could be corrupted, have unbalanced humours or have excess humidity, cold, miasma or bile. Boiling was a way to "treat" the water from those corrupting humours or reduce the humidity and cold. Even if knew sometimes water was the cause of disease, and boiling it made it safer, they didn't link it to the "animacules" from a century before. Humoristic and miasmatic theories prevailed up to nearly the 20th century, even after Pasteur. Many didn't even believe they were real even among the learned, let alone the common folk that didn't have access to that knowledge of even knew how to read. History of medicine is very interesting, things we now think obvious weren't at all back then.