esshup may have a suggestion that involves "Cat litter".. We'll see if we can get him to elaborate. If nothing else, there's always aquacide pellets.
I wanted to use a herbicide to get down to the roots of a plant in the pond, so I used a liquid herbicide and a mortar mixing tub. I threw in about 1/2 bag of clay based oil dry, and mixed in the liquid herbicide. Then let it sit for a day, and broadcast it into the pond in the area that I wanted to kill the weeds in. It worked, but it wasn't a permanent fix, I had to re-treat the area in about 4 months.
Having a flow thru pond to treat, that will be difficult.
