The substitute for clean drinking water was "small beer", a brewed ale with about 2% alcohol. Much safer than drinking water from the pump; or, heaven forbid, from the River Thames, which in those days was even more of a sewer than it is now. You'd have to drink a lot of it to get drunk.
TFA describes a murder that happened in "the parish of St. Aldates". St. Aldates Street runs from the centre of Oxford downhill to the Thames at St. Ebbes. St. Ebbes itself was a slum; wealthy people wouldn't live next to a disease-ridden open sewer. The side-streets off St. Aldates are all narrow, dark mediaeval alleys.
Also alcohol in beer does nothing to 'clean' the water (how would that even make any sense?) it's the boiling that kills the bacteria, parasites etc. (and people have understood that boiling makes water safer for thousands of years if not more).
Because alcohol is toxic. This is also why there's a maximum alcohol concentration above which you need distillation: the alcohol kills off the yeast that makes it.
2% may not be enough kill off everything (I'd be surprised if it was), but in the absence of better training on my part (I'm not a biologist), I would assume it would still make a difference.
Alcohol and low pH might significantly slow down the risk of bacteria spreading. Which is relevant if you want to store.
Obviously it's not really that relevant if were talking about making the water safe to drink in the first place because boiling is much more effective.
And again the claim that medieval people drank beer all the time because all the water they had access to is dirty is a myth..
Ensuring access to clean water was something medieval people took very seriously with very severe punishments for those who polluted or tried poisoning sources of drinkable water.
People drank beer because it tasted good and was full of carbs (energy for the day). They even had small beer for breakfast.
I think this is a big difference.