A colonization trap takes many forms but essentially is a bag of rocks left in the pond for a month or more. Mud is hard to sample. Sugar floating works sometimes, otherwise you're stuck with tedious poking through the muck. Rocks can be shovelled up and washed over a net. A surprising number of amphipods and isopods can be caught this way.
Fastest method is to sweep net just over the substrate and through the vegetation.
This works just like terrestrial systems except you use an aquatic net. For live specimens, collect everything into the same pond water. Keep in mind half of what you collect will eat the other half, given enough time. In flowing water, you stand upstream holding the net on the creek floor downstream and about 1.0-1.5 feet in front of you. You can also use this net in ponds or the littoral regions of lakes by sweeping it back and forth through the water dislodging the invertebrates from the vegetation and creating your own current to carry the invertebrates into your bag.