It should be fine, yes, but I think that largely depends on the size of charger you have. I have a bank of two batteries, and the charger is connected to one of them, so yes it will work fine, as that is how most boats do it. If you only have a very low capacity charger, though, I think it may struggle a bit. From memory I think mine is a 30 amp dual bank charger, which feeds 1x 85Ah battery on the port bank and 2x85Ah on the starboard bank.
My old boat had 3x110Ah batteries on the domestic side which were charged as one bank from a charger with higher capacity, but I can't remember what it was!