It'll eventually clear on its own, but if you want to hurry it along, you can use a flocculant to bind the stuff so that it can be more easily picked up by the filters.

The color of the water sounds like tannins. It is usually from peat moss in potting soil, fallen leaves or run off from bark mulch.Tannins don't usually go away by themselves. Activated charcoal like that found where they sell aquarium supplies works well to remove the color and odors. Put it in a porous container where there is a strong water flow. An old cotton tube sock works better than a nylon stocking.

If there is a build up of ammonia, Ammo lock works along with the AC which also reduces ammonia. Water changes can reduce the stain and ammonia, too.

If the color is caused by mud it is a whole new ball game. To check for mud put some pond water into a glass jar and let it sit for an hour. Mud and other debris will settle out or float. There will be a layer of clear water. You can do a partial water change and then use quilt batting to filter out the debris and mud. Put the batting in the filter or in a garbage can with a two inch pipe through the side of the container near the bottom. Place the can near the edge of the pond so the pipe can reach over the edge. Pump the water into the top of the can so it runs through the batting. Cleaner water will come out of the pipe.