The simplest way to add a water level sensor (assuming it’s a simple on/off switch) is to connect it to the rain sensor port, and define it as a normally open rain sensor. This way, when the water level sensor closes, it disables watering (or if you want reverse logic, define it as a normally closed rain sensor).
Of course this might not satisfy your need, in which case you will need to modify the firmware slightly according to your need.