I get questions about pond vacs all the time. People want to use a pond vac or a wet vac to clean the bottom of the pond and not have to do a total clean out. And will that work? In a word, no.
A pond vac sucks up water. It sucks up the junk at the bottom of the pond, but it sucks more water than junk.
The other big problem with pond vacs is that they do not have enough suction to reach from the top of the pond where they must sit to the bottom of the pond where the junk is. Wet vacs are better at this, but still not the best.
If you want to clean the bottom of the pond and not pump all the water out of the pond first, try this: Go to the swimming pool supply store. Find a gadget that looks like the picture in the link above. Do not buy the mesh bag that the salesman wants to sell you. It doesn't work because the mesh is not fine enough. Also, if you don't already have a telescoping pole for your fish net, buy one of those as well.
When you get the saucer/vacuum cleaner home, attach your garden hose to the fitting on the saucer and a leg from an old pair of panty hose over the hole in the middle of the blue saucer. You now have a water pressure powered pond vac that will (sorta) clean the pond bottom. At least it will do a better job than the ones you pay lots of big green dollars for.
Put the saucer on the bottom of the pond. Turn on the water. If you turn the water on first, you will start the job wet.
Using the pole, which also has a handy place to attach, start vacuuming the bottom of the pond. The panty hose will fill up fast with all that pond scum on the bottom. You will quickly have a panty hose leg full of decayed plant material, fish waste and other unspeakable stuff that drops to the bottom of the pond.
When the panty hose leg gets heavy, turn off the water and empty the panty hose leg. Repeat until the bottom of the pond is as clean as you want it.
By the way, I put a water shut off valve at the saucer end of the hose so I can turn off the water without having to walk back to the hose bib every time.
This is a dirty, messy job. Wear old clothes and be prepared to shower immediately after.