I am assuming you are talking about the Muck Away pond treatment.... It is supposed to be a natural supply of bacteria. It may help... It might be something you have to do every year. Basically you are adding a butt load of the bacteria that are already in your pond... instead of adding them in huge amounts for them just to end up dieing try thinking of ways to create a place for them to live. A hot pond in full sun has less dissolved oxygen. The baterica can only breed as long as there is enough oxygen for them to keep doing so and tend to like to breed on surfaces. A rocky waterfall is a great habitat for them especially in a shady area. the more lumps and bumps the better to help churn up the water. The little particles floating around in the water are also places for the bacteria to breed... I would leave it going maybe add watter lilies if there is a good shallower place. They will help take up nutients too. Have you looked at any of teh natural swimming pool info... some really amazing setups. Notice the planted area to swiming area ratio.
Natual swimming pool
I would bet if you didn't fertilize for the rest of the year that the pond would clear up once the algae ran out of food (nitrate).
What lead you to the permies forums BTW?