You can usually set an offset (used to alter the reading to take the depth the transducer rises at into account - 1 or 2 feet normally), but that doesn't sound like your problem.
How does it read at more normal depths? anywhere near right?
The unit reads the delay between sending a pulse and hearing the echo and converts that to a depth. Shallow depths may get the return too quick to read. If that's the case, I don't think there's a lot you can do about it. Playing with the transducer angle might help, as might playing with sensitivity of the unit.
Mine (Lowrance HDS-7) basically just shows no lock when it gets really skinny.