Well when you deal with water, your bound to get wet.
If it isn't already drained, you could start by vacuuming the bottom of debris. I'm assuming you're familiar with the plastic siphons that are used for this purpose. By doing this, you'll be vacuuming the debris and drain out the old water. You can have it either draing into a 5 gallon bucket if you have one, or into an empty spot in the yard if you want.
Once that is done, you might need to scoop out leftover debris with a cup or any non-sharp tool, if your pond is made with a liner. Then, if you have an outdoor hose and have one of the pressure control nozzels on it, you can pressure clean the bottom with a jetstream of water. I wouldn't do this until the pond over flows though, only until all the dirt and debris are cleared off the liner. Then you'd have the scoop that water out with a cup.
You might get a little dirty, but it will be worth the payoff of a nicer pond. There may be other suggestions out there on how to do this, but this is just what I myself would do. I'm glad if I could help, and I hope you have good luck starting your pond up again. ~Angela