Your UV filter shold be taking care of the green water, and to a degree the the other algae as well, have you changed the bulb resently?? They only last a year or so.
There are a number of other things you can also try to lessen the amount of algae. Water changes, through a bit difficult with that much water. Lots of plants, they will use the nutriants that the algae is currently feeding off, and shade the water stopping the algae getting so much light. You could also add a filter to the input of your return pump, this could be as simple as a plastic container (ice cream container? but the bigger the better) with holes drilled and full of filter wood or sponge or some other filter media.
If your unable to syphon the crap out from the bottom of your pond I can't thing of many ways to clean it out. You could empty each pond, one at a time leaving a few weeks between. Or use a pump to suck all the stuff out. But my pick would be to add lots of plants and call the crap on the bottom plant food.