Clay has been used as a lining for all sorts of water containers from water
holes for domesticated animals to the lining used for canals and other man-made
waterways. I suggest patience, though I'd suggest turning off any water pumps
(if you have them fitted) until the clay particles settle out. They are
incredibly small and take a while to settle. Having any water flowing through
a water feature will mean that this process takes days, or weeks rather than a
day or so. I'm not sure as this advice will help. I don't really have enough
in the way of details to give you any really helpful advice. I wish you all
the best.

Dave.