If you are seeing the mussels (larger 2"-4") on the bottom and not attached to surfaces under water like dock posts or larger rocks the mussels are not zebra mussels and very likely native mussels. Most US mussel species similar to shiner species live in streams and rivers, however a few are adapted to live in ponds and lakes.
IMO the clearing of the water is due to loss or reduction of hardness (alkalinity) which causes less phytoplankton and making the water appear clearer. Your pond likely need another application of lime and fertilizer if you want more phytoplankton.
Last edited by Bill Cody; 04/15/18 10:22 AM.
