Does your water have a brown tint to it? You can see your fish, but the water's just not quite gin-clear, and is a bit tea-colored? Sometimes that can be attributed to a tannin effect: like dipping a tea bag into water for just a few seconds, it discolors the water. Tannins come from the leaves or flowers of a nearby plant, or perhaps even the water filling the pond, especially if you're on a well and not city water.
This is a naturally-occurring phenomenon that is not hazardous to the health of either fish or plants. Typically, this can be easily cleared up with activated charcoal. You can purchase activated charcoal, place it in a net bag, and add it to the biological filter on your pond. This may need to be replenished occasionally, but should do the trick within a few days.