Sounds to me like....1) one of your potted pond plants has been tiped over , or your fish are diggin in to them. 2) your pond maybe getting runoff, say from rain running into an uneven side into the pond. 3) If it has a pond liner you may have a hole/leak allowing dirt into the pond. If the fish are digging into the plants you could top the potted plants with pea gravel to help keep the soil in. If the pond is older than just this spring, you could have a sludge/mud/muck build up on the bottom. When the fish swim low they could be kicking up the gunk. If the waters more of a greenish murky tint you could be overstocked, or overfeeding or need more plants to keep up with the fish waste. Good luck.