PUMP OUT IS WORKING EFFICIENTLY BUT FRESH WATER IS NOT COMING IN.
Siobhan did you check that the intake is not plugged,close the seacock then the other thing is on the Jabsco toilets there is a rubber "O" ring that gets dry and will not pump anything in, the thing to do here is the 6 screws on the top of the plunger,undo them then pull the assembly out slowley,now take some vaseline and put it on the "O" ring and put some on the inside of the tube where the plunger, or you can go buy a new kit for it and it will tell you to do the same thing, the key here is to do this every year and you will never have problems, the other thing is baby oil will help during the year, pour some into the bowl and it will lubricate the "O" rings , I do mine in the fall here up north because people don't realize that where the lever where you flip to empty the toilet without water coming in is where you took out those 6 screws a cup of water sits in there all year and freezes in the winter so I use a shop vac suck out that water and lube that seal and it's done for the next boating season good luck :-)
Myles advice is spot-on.
Just to clarify, you say "fresh water" so can we assume your head flushes with fresh water from a tank aboard? If so, check the line that feeds water from your tank to the toilet. ( Also make sure there is water in the tank! ;) )