Your roots just need more air, if you are watering too much with that small of plant in that large of container, the roots arent big enough to suck up all that water all over the container, you must picture your roots as being roughly the same size as your plant.. only beneath the soil, that should give you an idea on the area of space your roots are taking up. Roots love air, thats why hydro works so well, the more you let your soil dry out with out allowing the plant to wilt from over dryness, the better...
as per your question, if you keep suffocating them it will lower your productivity, wait a good 3-4 days for your next watering