I use an old shop vac that I picked up at a yard sale for $5 to clean the debris out of the bottom of my pond and filters after I have pumped most of the water out. It only has about a 3 gallon capacity but it does a great job of pulling water and everything else out, even the fine silt.
They make regular pond vacs that you can use to vacuum debris out of your pond without draining it down - I have never seen one and they are advertized somewhere in the $250+ range.

I found a bunch of pond vacs at amozon diffrent types in all price ranges. Check it out.

Here is a link that might be useful: Amozon pond vaccums

I just got the Hagen Laguna Pond-Vaccum that hooks up to the garden hose & faucet. The long handle & nozzle on the end has a conveniently located on/off switch to turn the water on or off there & there is a net bag to collect the debris that is sucked up. The problem is that the water circulated through the bag stirs up the bottom sludge too much & the water horribly murky & if the valve is wide open the water flowing back into the pond soon would overflow it!!! Now the shop vac I tried did the opposite: it was too powerful & emptied the pond quickly ... hard to control the suction as no close on/off switch to use other than the switch back on the cannister. I hope we can make some adjustment on the Hagen Laguna vac so a hose can be attached to the place where the bag attaches & then run the water out into a tub or out on the lawn so it doesn't stir up the goop in the pond! I'm asking the company for ideas ...