Thicker sub-base could be part of the fix, but it's not a one size fits all solution. I've seen something similar with clay stains ruining the pristine white sand in golf bunkers.

In a general way, it's usually easier to change the water part of the problem than to work with the clay. This type thing is site specific, meaning what works in one place doesn't in another. Without a lot more detail, that's about all I have for you.

Thank you.

The site is pretty flat at the area I am going to have fresh gravel surface. Is that what you are asking for for the specifics???

change the water part of the problem???

If water is pooling you need a slight slope to direct it away. I'm only mentioning that as a general observation, because I couldn't possibly tell you how to slope the ground or where the water should go.

from the description,I'm envisioning shallow "bowls" of water that are filled level with gravel. When it rains, they fill up from the natural runoff. When the water finally seeps away, stained gravel is what's left behind. Is that it? If so, then the "bowls" need a hole "punched" in their side so they can drain. Essentially, I'm seconding catkim...there needs to be an always present way for water to get out so it doesn't collect in the first place. For some specific suggestions, you might post a photo or two that clearly show the conditions. (Post photo html code from your photo-hosting site directly into the message of your post.)