Let's say you're in Africa camping and your source of water is a 'puddle' of water. The water is murky, and the source is less than 2 feet deep, so I wouldn't call it a well. And it doesn't have a regular shape and scattered all over it are some bushes. The water is replenished by underground water just like a well. I know it's disgusting but that's what the natives drink, of course after boiling it. Also, I won't call it a stream just like I won't call a well a stream because the water doesn't flow. I wonder what you would call it, a patch of water?

I hope my explanation is clear enough for you to picture it. I can't find a picture on Google Images because I don't have a name for it.

Or perhaps a "waterhole" or a "pond"?
A waterhole can be quite large.

I think it is a good word here though - or spring. The water is supplied by a spring (underground stream reaching the surface) in your description.
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You might say "a spring".

 Feebs11's reply was promoted to an answer.

Here's a picture of a spring I found on Google Images.

Do you have a word that carries negative connotation because it's really murky, and looks filthy and disgusting. The spring in the picture is too good compared to the one I would like to say.

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Is a waterhole smaller than a pond and a pond is smaller than a lake?

I think waterhole is the best option. By the way, according to my dictionary, a spring is not a still body of water so I guess it doesn't fit my description.
 nona the brit's reply was promoted to an answer.