There are 2 things I've seen that work, one is to put a syphon break (essentially a small hole that'll let air in) into the intake pipe, that way, if the water level drops then the filter will start to suck on air. Alternatively you can simply terminate the pipe higher in the tank, but that'd mean that it takes from the top of the tank, rather than the bottom.
The second part of this is to put a float switch on the power supply to the filter, otherwise any break will burn out the motor as it tries to run on air. Can also be run to an alarm if you're wiring minded enough.