You can do one of two things.
First create a loop that backtracks on itself around the entire yard excluding the water front. Start by running the outer loop starting at the power source. then when you reach the water on the far end come inside the first line by about three feet and track all the way back around to the power source.
The second option you still need two loops to achieve but you would twist the wires together, 10 twists per foot will cancel the signal to the collar. this is not a lot of fun to do if you have to go a long distance, but you would need to do this to allow the dogs to cross over the line from the outer boundary to the power unit.
These are the only two ways that you can leave a dead zone in the loop, conduit and metals will not cancel the signal and even with the twisting if is not tight enough there are still spots that are live.
http://www.gundogsupply.com/inguandfaq.html Installation number five would be exactly what the first option would look like.
Hope that helps, these systems are great and the dog loves the free roam and we love the fact that we do not need to worry about the dogs running all around the neighborhood.