I would start with bringing alternate power from your battery that you know has 12 volts directly to your water pump. If that works, then you should check the positive side only with your alternate power, then the negative side only with your switches on. That will determine if it's the power going out, or going back from the pump. If the pump does not work with both wires connected to your alternate power and you know your power works because you have tested it with a light, the pump might be shot.
Those are the easiest checks to make without a doubt, so start there and let us know what you find.