Unfortunately when dealing with pests you have to research and find what you are looking for to get the right course of action.
If you could kill one or trap one then we could help you identify them.
Are they Normal house flies?
Are they Fungus gnats?
Are they white flies?
are they green flies?
Are they living in the top of your soil?
You could try getting yourself some sticky yellow traps to see if you can catch one.
If they are fungus gnats the best course of action for you would be to get something like spinosad as this is a bacteria that pretty much pulverises any pest.