It might be possible that the sago pondweed is providing a shallow substrate upon which the filamentous algae is growing. Algae can, and will grow on submerged plants that are contacted by sunlight.
Unless you've identified that algae is indeed growing on the pond's bottom and then rising to the surface as it matures, my guess is that the sago is providing an artificial "bottom" for the algea's proliferation.
If so, then your efforts should focus on controlling the sago. I'm surprised the grass carp aren't doing their part. Might be that they need some help to get ahead of the sago's growth-curve (ie. knock it back in selected areas with a contact-herbicide, such a REWARD, KOMEEN, NAUTIQUE, etc).
