For those who can't stock Tilapia do to regualations or because it is just too cold like up here in NY I would suggest that you try pond die.
We had a terrible problem with FA last year. This year my pond expert at catskill pond, Scott Trava had me use blue/black pond die. Even with the harsh drought we had this year we had no FA at all.

The theory on this is that he die reduces the light penetration enough to disrupt the growth cycle of the FA. For the less than $50 cost of the die per acre of pond size I would recommend you give it a try. I know we will use it again next spring.

It is non toxic and does not stain people or pets that swim in the pond once it is diluted.