We're getting ready to build our new pond. The contractor wants to
line the walls and bottom with rocks, which he says will serve as a
great huge biofilter.

The walls will be okay, but depending how you do the floor, the
rock may trap detritus and be difficult to clean. All that stuff
will settle somewhere, in this case between your rocks. I would
think this would be a maintenance issue you'd rather not have.

C//