I also have a 2 acre pond. By the time it was 4 years old it was FULL of naiad. I think I put in 20 grass carp in October. By the following June the naiad was all but gone. No dyes or chemicals whatsoever. Probably not what you want to hear but I think the FA problem got a little worse.
2 things here.. #1, start with 2-3 TGC per acre.
#2, when the aquatic vegetation that burns/utilizes nutrients is gone, the nutrients become available to form algal growth, hench FA or worse, Chara..
Small steps at a time.
