Fuses are typically as close to the power supply as possible. Since this is a 12v pump, it would be either directly wired to the battery and a few inches from there, or into the 12V bus, which would have it's own fuse. The fuse protects the wire, not the device.
Get a volt-meter and test the circuit, then start tracing it back to the source (e.g. 12v bus or battery).