1 - 2 inches is ok... 1.5-2 is better because if you can see the water then sunlight can get where algae like to grow. Also some bugs like to lay their eggs in nice warm & moist habitats.
That helps a lot, Jonathon. Thanks!
Aquaponics is pretty flexible and sometimes it is handy to have the water level a bit higher to help start seeds and for some plants you want the water level lower but the main rule is that the top of the media stays dry to protect your water from excess evaporation and algae growing. And inch or so below the top of the media is the general rule and beware that a new system the media is likely to settle a bit so having an extra bag or pile of media handy to top up the surface might be a good idea after the initial media settles.