We had quite the algae bloom this Spring - even clogged the pipes from pond to filter and they are 4'' pvc. The poor alligator couldn't spit! waterfall nearly stopped. Worse mess we have seen in a few years. But, all is well again now. As quickly as it went 'green' - it cleared up again. I do add bacteria to my filter each Spring and add bacteria to the water every few weeks - one kind for warm season and another one for colder weather.
We have a 70 gallon home made bio filter that hides behind our lilac bush and it does a great job. We built it about 5 years go and have only cleaned it out a couple times. Basically - shaking the goop off the media and putting it back in and removing a bit of the gunk from the bottom. It works best when we ignore it.
Here's the link if anyone is interested.
http://www.skippysstuff.com/index.html It was the BEST thing we ever did for our pond and ourselves.
Funny thing - our first pond had no filter, no pump - just plants and fish and was perfectly clear as well. Guess we hit a good balance there too. It did go green in Spring for a couple weeks but always cleared up by itself and stayed clear. We always toss a couple of water lettuces in each Spring and sometimes water hyacinth - they help shade the pond and keep it clear. One year they did so well that I sold them - sold enough to cover the cost of all my Spring yard planting that year :0) I would just meet folks at the parking lot of a warehouse store after work a couple times a week. Advertised on C's list online for free. Retired now so I just put extras into the compost pile.
