Alum (Aluminum Sulfate) will clear up the muddy water if the cause is due to water chemistry issues (but use caution if fish are present as it may cause severe pH swings). However, alum won't aleviate a physical issue (wading livestock, fish "rooting up" the bottom, disturbed soils in the watershed being washed into the pond by rain, etc.).
So, presuming that you've confirmed a chemistry issue AND know how to avoid pH swings, you should also be aware that resuspension of the "flocked" clay particles is possible - but usually associated with a physical disturbance. In most situations of which I'm familiar, retreatment was necessary if/when a resuspension occured.