Are we talking about "free-floating" or what is also called "suspended algae"? When your pond has pea-soup colored water, i.e., green water then we are talking about free-floating or suspended algae. Most of us don't like that kind because we can't see the fish. Then there is "string algae" or sometimes called "hair algae", often a good sign of healthy water but unsightly. String algae is often several inches to a foot or more long. And then there is the common green algae that grows on everything in the pond and that type of algae is completely normal.
Assuming you are talking about the free-floating algae, the trick is to starve out the floating algae. Floating or suspended algae feed on nutrients in the water. Nutrients are primarily provided by fish poop, decaying plant material on the bottom and fertilizers used to feed your potted plants. Free-floating algae thrives on sun and nutrients in the water. Thus, reducing the amount of sun or nutrients causes it to disappear. Changing the water usually justs compounds the problem. Once a pond becomes "balanced", this free-floating algae problem should go away. Pond "balance" just means having the right amount of plants, both oxygenating plants such as hornwort or anacharis, the right number of fish, and the right amount of shade either from overhead shade or shade producing plants such as water lilies.
Another way many pond keepers keep their pond water clear is by the use of a bio-filter. A bio-filter is a device that contains media (rocks, gravel, plastic media etc.) for microbes to grow on. The microbes will feed on the nutrients in the water and starve out the free-floating algae. You mention that you have a filter. It sounds like it may be a mechanical type filter used to screen out junk to protect the pump and not necessarily designed as a bio-filter. However, event this type of filter will act somewhat as a biofilter. For example, if it is a sponge-type of filter, the microbes will grow on it and be helpful in feeding on nutrients in the water. If you have a sponge-type of filter, don't clean it with chlorined tap water as that will likely kill these beneficial microbes and it will take a few weeks for them to regrow. Use water from the pond in a bucket to clean the filter.
Another way many people get rid of free-floating algae is by zapping the little rascals with a UV Sterilizer. This equipment is often located with their bio-filter. As the pond water passes through the UV Sterilizer the high intensity ultraviolet light will kill the free-floating algae. These devices are extremely effective in killing off this type of algae.
I hope I'm not giving you too much information to digest. I will leave you with a link to a reputable pond supply business that will have bio-filters, uv sterilizers etc...
http://www.azponds.com/default.htm?source=google&gclid=CMDw_NWv2JICFRItagodJzeL-g
