When your pond water is green (and it isn’t St. Patrick’s day) it’s most likely because of single-celled algae.
The green color comes because this kind of algae remains suspended in the water. When the conditions are right in a pond with lots of sunlight & nutrients, as many as 5 million (!) algae cells can be in each milliliter of pond water (that’s only 1/30 of an ounce).
These organisms are obviously very tiny. They’re so tiny that they’ll go right on through even very fine filters.
The trick is to use a flocculant to help filter them out. Flocculants make the small particles stick together so that they’re large enough to be caught in the filter. I really like the new Rapid Clear fine filter pads. They’re a disposable filter from Aquascape made to be used with a flocculant.
Be careful, your filter pads will clog pretty fast. When I use a flocculant I also like to use a sludge and filter cleaner, too. The bacteria in the sludge cleaner tracks down those chunks of algae and eats them.
Once things are back under control, I keep them that way with a regular use of beneficial bacteria (the dry is what I recommend for regular maintenance since it is the best bang for your buck).