Groundwater?

So I have discovered that there's groundwater about 2-3 inches deep about a foot and a half or so down in some of my plot holes. If I cover with a layer of rocks, will they still be useable?

Say what???

I mean to say, some of my holes I've dug out to fill with soil and plant in have about 2-3 inches of groundwater flowing through them. If I layer the bottoms of said holes with rocks, will I still be able to use them? It's a drainage issue that's worrying me.

Most who have standing water cant go in the ground. Raised bed, an pots ect..........