Is this a massive overreaction?

I think you need to ask what has caused all of this. If you can’t speak face to face then write. Maybe he knows that he over reacted but doesn’t know how to back pedal or maybe there is a real problem and this was just the straw that broke the camel’s back.It may be a mixture of feeling neglected and resentment that you have a new friend group, or it might be that he thinks your behaviour has genuinely been out of order given that you have found a group to party and drink with on a regular basis.
Just as a little side note as the mother of 3 young adults. When they’ve come back after a night out having had a glass or two ( or 3) too many, they genuinely believe that they are being as quiet as church mice but it’s more like elephants trying to tip toe and failing. Drink does change your perception of the noise you are making, so if you have repeatedly come back late and woken the house up he may just have seen this last episode as the one too many.
Whatever, it’s a shame to write off a friendship like this, so have an honest exchange to clear the air and find out where you really stand.
Hoping things work out in a way that enables both of you to move on without regrets.

Honestly I think this has been quite a toxic friendship and I just was ignoring all the issues so I don't want to put in anymore effort... its just not worth it, like I have been feeling quite drained speaking to him on various occasions and that is just not nice to be around

This doesn't sound like it's only happened the once. I'm getting the impression this has happened many times and he's just lain in bed silently stewing over it each time rather than say something. He explicitly asked you not to get water, so I imagine he can hear the pipes in his room. e.g. I can hear when any of my flatmates turn on any tap in the house because my girlfriend & I have the room closest to the hot water tank - and yes this can wake us.

Talk to him and figure out if this has actually been a long-term issue he has simply remained silent on. You can figure out a solution from there, e.g. leaving a bottle of water in your room before going out at night. Work to resolve the issue rather than being defensive or hostile.

That's the thing, I have been leaving bottles in my room etc. and have made genuine efforts to limit the time I have spent disrupting and have also asked if this has been something that he has just been silent on but he just is not telling me any other instance when this has happened. So this is my problem, I don't know if this has been a long tern thing... I've asked more than five times and all he's managed to say is the one time I got water around 11:30 a few months ago. He himself slams the doors really late at night but does not see that as inconsiderate and has yelled at us all throughout the course of the tenancy, this isn't the first time there has been conflict with this flatmate for similar issues, his old flatmates left him for the same kind of behaviour where they were just done with his constant yelling so idk really. I have admitted my mistake and apologised multiple times so I don't really know what else I can do to be honest

This seems to be an about turn on who is in the wrong. You’ve convinced yourself that he is the one being unreasonable and so managed to exonerate yourself of any blame. In all probability he is stressed and is overacting to this one last episode, but it also sounds to me from all the little hints that you have been dropping throughout your posts, that you have lived your student year as you wanted to, with little or no consideration for those around you.
You can walk away and say good riddance if you want to, but as I’ve already said, it would be so much nicer to finish the year on a nice note. So send a genuine apology. State that you hadn’t realised that you had been inconveniencing him and that had you known you would have made every effort to avoid doing so.
If, as you implied, all the others in the flat are on his side, then there must be some truth in what he’s stating.
If you can’t make it up then move on. Let it be a lesson for you when you’re in another shared flat or house.

If you have apologised there is nothing more that you can do. Just try and finish the year without any major fireworks and then let him move on. Sharing accommodation is not always easy. It’s an exercise in compromise and if you can’t communicate honestly then it’s unlikely to work. You gave it a go and there’s not a lot more you can do.