Hi Matt,
Why not use a float switch to cut the power to the master pumps? I’d do it independently of the RPI. Just put a float switch on the power supply to each pump. When the reservoir is empty, the power gets cut to the pump thus preventing it from running dry.
If you want to keep tabs on the water level in the reservoir, I’d consider using something like this to keep track because it’ll tell you how full it is, not just is it empty or not.
Mike