Other factors apart, I expect the pervasive presence of Giardia in almost all fresh water in the North contributed to the high mortality rate among people living there up until the twentieth century, especially infants & young children. So 'how did people manage for thousands of years?' Answer, they were often sick, or died, so that together with a harsh environment generally, the population was quite small and thinly spread.

Of course this isn't the only contaminant in the water, but is one which can't be blamed on the people themselves as self-inflicted, as might be the case with eg coliform bacteria (though it's doubtful if anyone dirties their own water given an option to avoid that).