There is a natural BT listed for Gnats, and you are right in assuming the larvae are eating the roots. I think it is named Gnatrol and should be easy to find. Al

I know gnats thrive on a wet surface, so try spreading some vermiculite over the pots. it's decorative and it works for me (I have a thin layer of vermiculite over all my pots and haven't seen a gnat so far for the past few montsh)

It's tough when you need a moist medium, the gnats are attracted to moisture.

The BT that will work for you is BTi - bacillus thuringiensis subspecies israelensis, different than the biological control available for caterpillars.

Available in liquid form as Gnatrol and Knock Out Gnats, or you can make your own from mosquito dunks. Float a dunk in a container of water overnight, use the water to water your pots for at least three consecutive waterings, timed as you need to keep adequate moisture for your plants. Save the dunk to re-use, intermittent wetting and drying doesn't alter the effectiveness.

I mention the dunk because liquid products aren't available locally to me here - although I do keep Knock Out Gnats on hand now. The liquid form BTi gives me the option of mixing to the strength I want - the dunks will work in a pinch.

I have tried a tobacco spray to kill bugs. It works great & I have read that it is really effective as a soil drench.
I think I like morz's use of the mosquito dunks better though. I wonder if I could spray that for aphids & such?

Kate, I wish it did work as well for other critters as it does mosquito larvae and gnats :)

Bti is a naturally occurring soil bacterium.

It is specific to mosquitoes/gnats, blackflies and midges and is essentially non toxic to other insects, birds, humans, mammals

I switched to bottom watering and ended my fungus gnat problem. I let the soil surface stay dry. I grow in deeper trays than most people and I either sink a small plastic pot down into the media and pour water into the pot or I set the tray into another tray and only water the lower tray. I've seen people use various fine powders sprinkled on the surface to keep it dry with some success also.

I use crumbled up mosquito dunks and just sprinkle it in the pots,and those yellow sticky traps the traps are only necessary because i wait too long to begin treatment.