Dredge
One way to sample what lies at the bottom is by using a dredge. This brass device will "bite" the mud off the bottom and close allowing you to bring up samples of what is there....be careful, you may not be allowed to do this in marine reserves.
One way to deal with the sample collected is to dump it onto a screen...in this case a soil sifter with many screen sizes can separate your sample according to the size of the organisms collected.
Dump the sample onto the screen, with the largest holes at the top.