My basement floor recently had some holes pop up... note that it popped upward and did not fall in. When I pulled back the peices of concrete I found that the hole seems to go down between 1/8" to 3/4" to dirt. Hole depths vary. The peices of concrete I removed also seemed to be very slightly moist. Any suggestions on repair? I was thinking to coat the bottom surface with a waterproof paint and then patch the concrete hole.

Question #1: what region do you live in?
Question #2: what is the soil like under your floor?
Question #3: why do you think "waterproof" paint will solve anything, and do you believe in the tooth fairy?
Question #4: how old is the house?
Question #5: how thick is the concrete in the floor?
Question #6: is there any sign of a vapor retarder under the floor, such as plastic film?
Question #7: what has the weather been like the last few months? Rainy? Dry? Above or below normal in any way?

I can probably guess at every answer except #3; I know the answer to that one.

1) DC
2) Hard soil, what other info would bbe useful here?
3) Not sure, it just looked like there was a red paint on top of the tamped dirt surface before.
4) 1895
5) between 1/4" to 1.5" thick... looks like a topping slab only.
6) no
7) No, not wet lately. Two years ago in the summer there were heavy floods in our area due to rain for 2 weeks straight. I had friends several blocks away with knee-high water. I only had about 1/4" inch, but that is when I ripped out the carpet and found a few of these holes. Lately, the weather has just been cold.

Thanks for your help.

If you want clean, dry, mold-free space, the best course of action would be to remove the concrete floor you have, dig down a little, place 4 inches of gravel, a polyethylene vapor retarder film, and pour a new 4-inch thick floor slab with 66-1010 mesh in it.

thanks for the advice. Any chance if you know the following:
1) the best method for determining if you can dig down the basement (ie am I going to hit my drainage system? I live in DC, so we have city sewer out front)
2) Average cost for such work.

Tough to answer such questions without seeing the house. The only real answer would be to dig mall exploratory holes to determine the depth of the foundation wall bottoms and any pipes that might be under the floor.

There is no "average" cost for such things. The best cost can be determined by having contratcors who have seen the house bid on the job.