A gardener writes in:

"We used 5 gallon buckets for our 3 tomatoes, 2 squash, and lemon cucumber plants this summer. I seem to have flies in the dirt! Am I over watering? What natural ways can I get rid of them?"

I'm going to take a stab and assume that the flies in question are gnats rather than house flies or white flies.  Given that, yes, over watering contributes to this problem.  It sounds like you have Fungus Gnats - little flies that lay eggs in the soil where it's nice and moist, then the eggs develop into larvae and new gnats.  These gnats are generally more of a nuisance than dangerous, however they can be a problem if they start feeding off your plants' roots and stems, which they tend to do in epidemic cases.  There are several ways to treat this, and I would suggest a combination of at least two of them to combat your infestation:

1) Let your soil dry out for at least 24 hours.  They can't survive in dry conditions, so you will brake the cycle of life and kill off the larvae.  I have to assume that your 5 gallon buckets have good drainage.  If not, make sure to prepare your buckets with several drainage holes and some gravel at the bottom next year.

2) Sticky Traps - some people have said that this works, others haven't had much luck, but it's worth trying.  Place the sticky trap either face down on the soil's surface or vertically in the stakes that comes with the sticky traps.  Change them as often as needed.  You can find them either at Gardener's Supply - (click the link below)


or you can find some more attractive ones at Garden's Alive.com.  Click the link below and type "Pot Stickers" into the search box at the upper left.  
 




3) You can use a natural larvicide that is added directly to the soil, inoculating it with larvae-eating bacteria called Bacillus thuringiensis (Bti), also from Garden's Alive. Click on the link below and scroll down to "Knock Out Gnats":