You only need to remove the positive cables from your batteries in order to use the multimeter to read their separate voltages. BUT, you must be extremely careful that when you are removing the positive (red) connectors, that you don't allow either end of the cable to touch the metal of the boat. This is dangerous stuff as the battery will short and potentially could do some very nasty things. Take an old sock with you and once you have disconnected one terminal, wrap it up well in the sock to isolate it whilst you uncouple the other end and remove the cable altogether.
Now you can take a voltage reading from the isolated battery as described above. If it's below 12v, then you can assume it is completely discharged. If so, best to remove the battery from the boat and get it properly charged up on a quality mains battery charger.
PS I had loss of distilled water in a couple of cells last year - to my astonishment, once I had filled the cell, and re-charged the battery fully, the battery went on to perform as normal. It just depends if any damage has been done to the plates inside the battery.
Good luck.
Philip