I have about a 1/4 acre pond, with a limestone block wall along one side, and pvc liner oround the rest, liner covered w/pea gravel. I started filling it last week, it's 3-4 foot deep now. It was clear to the bottom before a cold front came thru, with about 2 inches of rain overnight. Now the water is a milky green color, I'm suspecting some mineral is causing it. It's not an algae color green, more of a pastel green, with visibility of 1 foot. We have caliche and limestone, and I've also heard that copperas can cause a green cloudiness.
Where should I start to try and clarify the water? It has no fish at present, just a swimming hole for the family, but I'd really like to keep the water clear as possible. I use some chlorine in it, and plan to put in a floating fountain for aeration. Any advice would be appreciated.

DO NOT ADD CHLORINE!!

The turbidity is most likely a combination of planktonic algae and the rock dust from the pea gravel. You have what is called 'New Pond Syndrome' and the 2 inches of rain has exacerbated it be not only washing the dust from the pea gravel but most likely caused some run-off from the surrounding land raising the nutrient levels of the water column.

Aeration is always a good choice.

The problem should clear over time.

Clay in a weak solution will also cause a green coloration. So will iron but I doubt this is the case in your situation. Like Instar says it should settle out.

It did get crystal clear, for a short time. Then it rained, got a little murky, and before it could settle out, I got some algae growing when the weather got hot. I have a fountain, but wondering whether an aerator ( airmax am10-sw) or some algae control chemical would help (or both?). Any help from the more experienced would be appreciated.

Why did you advise against adding chlorine? Thanks

Green Cloudy water formed due to scattered green algae cells on water surface and make it look ugly.
There are some biological products available in market that are effective solution for the problem and does not affect filter or aquatic life.

Chlorine will kill most all aquatic plants and bio-accumulates in the pond.

See this http://forums.pondboss.com/ubbthreads.php?ubb=showflat&Number=349570&page=1