clay/dirt bottom?

What about using clay/sand in the bottom of the pond over the liner
and planting pond plants directly in the mud.  No pots and lots of
places for water creatures to live.  It would be muddy water after a
rain, but it should settle back down and be clear...right?  I couldn't
have a lot of water movement or it would never be clear. 1/2 of the
pond (deep end) could be just liner and the other 1/2 of the pond
could have clay.  This way I could have some filtration and movement
at the deep end with out stiring up the shallower end too much.  Any
thoughts on this?

Thanks for letting me think out loud 

Tracey