Question
Only 4 out of 14 sprinkler zones work. I found that one of the inground boxes containing the valves and wiring is under water could this be the problem?

Thank You

Answer
Yes, it could be that water has got into the wire connections at the valve.  Locate the connections (where the wires from the valve connect to the wires from the controller) and replace the connectors with waterproof wire nuts.  These are available at most places where they sell irrigation supplies.  If this doesnt work, you may have a more serious problem with either the controller, the wiring or the valves themselves that would require troubleshooting the entire system.