Not sure the rock makes much difference there, at least it shouldn't. Your clarity could be explained by your lights not being on. If you are driving in the fog your high beams will just illuminate the fog and reflect the light back at you, whereas your low beams will send light out under your range of vision allowing you to see past the fog. I'm thinking is it similar here where with your lights off you just don't see the particles in the water.
Your rock should not filter anything. If it creates dead spots then some silt could settle out but you don't want dead spots. Run some sort of a filter and try to catch as much of that crap as you can, even a hob filter stuffed with filter floss would help. Or turn your flow off, wait for it to settle, then siphon off the silt. You need some sort of manual removal where you can separate and then pull the silt out. If I were you, I'd try both methods, but mix up the sand bed first to get as much as you can.