well sadly I had a problem with super tiny little knats a while back, and had the hardiest time ever getting rid of them 100%.
A. Bleech all drains. mild solution mixed with warm water and then pour down all your drains. They breed their notoriusly.
B. They are probably the ones that lay their larva in the soil, which then eat at the roots of your plants, stunting them! Best solution is to cover the top of your soil with a thin layer of sand or realy small peebles (even perlite could work). I used sand.
C. Get the old school fly hang strips, but instead lay them horizontal (sideways) over your soil/containers. Works 10 times better and you get them as soon as they take their first flight.
D. check windows. oddly enough they can breed, live, and/or slip in through those too. Crazy little buggers. I found a bunch there as well.
There are other methods to treat the soil for the larva but natural old sand is the best IMO.
Also, you are likely slightly over-watering if you have these, as they need wet dark places to breed and can not live in the soil unless the soil remains damp.
hope that helps!