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They are fungus gnats and they lay their eggs in the soil and the larva eat the decaying matter in the soil and will also attack living roots. There are some drops called tanlin you can buy to add to the water to prevent this. There is something in the drops that causes the larvas guts to explode. It is non toxic to other creatures but using this along with yellow traps i see only the odd gnat now. You need to keep at it though cause if you dont they slowly sneak back. This seems to be a more recent problem. I never had this issue years ago.... If you have what you think are fruit flys also they are probably phorid flys.... Ideal food for tiny slings....