that we had to boil water to drink it

Not necessarily. While certain types of water should be boiled before consumption (a fact recognised by multiple writers of the past; Hildegard of Bingen recommends boiling river water before use), quite a few natural water sources are safe enough for human consumption without need of boiling.

I have a post addressing water and its drinking, as well as Medieval aqueducts. The latter are relevant because these aqueducts most usually bring in spring water from outside a town, again without need of boiling. Indeed, Exeter maintained its Medieval-era aqueduct well into the 1800s because its water was "was considered the best for tea and pea-soup" by the population. (Considering that the competition was the water-engines bringing up less salubrious river water, it's easy to see why.)

While the above posts are focused on the Medieval Period, water and its purity are the same everywhere, so I am reasonably confident of applying those precepts to pretty much everywhere on Earth, allowing for local variations. In other words, the answer is Option 3: It's not as unsafe as you think.

And since I know this place and I know how these threads go - it's not booze. Pre-modern people did not drink alcohol because water was unsafe; they drank it because water is boring and booze is fun. More on that in the first link.

Anthropology major, not a historian. Disease ecology is pretty fascinating. We have a term called the health paradox. When we look at the bones of our ancestors historical and prehistorical we can see the damage caused by disease (bacteria, viruses, and parasites) and famine. However, our ancestors often survive repeated instances of disease. So they are afflicted often which seems unhealthy, but are apparently healthy enough to endure hardship.

There are many places in the world that continue consume contaminated water. And individuals in the places can have constant pathological infections. They also have less allergies as their immune system is actually fighting off infections. https://www.immunology.org/news/molecular-mechanism-allergies-discovered

There is a concept of pathogen load in water. If you can imagine if one person soils a stream with their feces the pathogens are dispersed and likely die outside their ideal environment. A few pathogens especially parasites like worms actually require returning to a water source as apart of their life cycle. With the advent of agriculture the concentration of people around the same water increased. So when you use to have less that hundred people you now have the food capacity for ten to hundred times that amount. The capacity for the environment to disperses and remove pathogens has not increased so disease spreads through this oral fecal transmission route. Treating waste water drastically reduce human specific infecting agents. Naturally occurring pathogens still exists, thus the need for water treatment of which boiling is one method. Many cultures may have inadvertently treated their water without any knowledge of germ theory. Diluting alcohol into their water, preferring fermented and/or hot beverages, useing botanicals with anti microbial properties, or drinking animal milk. Knowledge of 'bad' water sources is also passed down without the full understanding of why the water is 'bad' by our understanding.

So one answer is there is less need for water treatment if there is less human waste in water. There are still numerous disease reservoirs that don't need humans to spread. The variables that effect this are too numerous to name but if can imagine the difference between a snow melt stream from a mountain and a stagnant pond algae green pond you can start to see how risk factors increase from environmental influences.

The second answers if you grow up in a high pathogen environment your immune system may adapt, but it may not be pleasant. Evolution also plays a hand in this as genes that help your survive the infection are passed down and those that die before rearing child may not of had the right genes for the selective pressure.

There is also developing research on our microbiome especially in the gastrointestinal tract. If you have a strong and diverse microflora in your gut it might prevent infect by out competing harmful microflora. We can only make inference on historical and prehistorical populations based on diet. You should know that the western diet has poor diversity and leads to inflammatory disease. Again the advent of agriculture probably had huge impacts on a population's gut microbiome which again is very hard to study in historical and prehistorical populations.