Take a 5 gallon bucket lid and screw it to a PVC endcap. Put that on a PVC pipe and shove it into the pond bottom as hard as you can. Measure from lid to water mark on pipe. Do that in a few places. Now, remove lid and see how far you can shove the pipe into the bottom. Difference between the 2 measurements is what the muck level is.
A muck removal company told me thats how they estimate how much muck has to be removed, since they charge by the cubic yard.