Hi Tim, this would normally be an agreement with your landlord. Unless your rental agreement included all bills, then you would be expected to pay the water charge.
There would certainly have been water bills sent out during that 3 year period so I would ask you landlord why he has only just started to pass the charge on to you. As an aside the water billing has had a major overhaul this year and its a lot clearer than it used to be, so it may just have been that your landlord hadn't realised the water charges were just getting added straight to his service charge account.
Hope that helps.