Large zones of weed killing will cause a depletion of oxygen as the dying weeds rot. You will have to check with the manufacture on how large a percentage of the pond you can kill at a time...
Depending on the size of area, I have know of people that have sunk black mats or plastic to prevent light penetration in the area they want open either by lowering the water level or by creatively sinking the mats.
They also make pond dies that will block the light from getting down to the bottom, retarding weed growth. This would be a waste of money of the water is constantly being replaced by a feeder stream and spillway.
They make a weed cutting blade that looks like a "Y" that you can drag behind a boat or throw out and drag through the lilies the "V" section has very sharp blades but, by hand its a lot of work!
http://www.thepondguy.com/product/jenlis-weedrazer-aquatic-weed-cutter/aquatic-weed-removal-tools
http://www.thepondguy.com/product/j...quatic-weed-cutter/aquatic-weed-removal-tools
There are two options for chemical use. Pellets or spraying a killer specific to the weed in question.
The pellets are hand broadcast in the spring and attack the plant before it hits the surface. *** I have found this to be a waste of money if you have a really mucky bottom as the muck will "encase" the pellet and prevent it from being absorbed by near-by root systems.
The spray herbicide is applied in the spring as the lilies hit the surface. Its a liquid mixed with water and a kicker (a soapy type additive) that helps the spray adhere to the lily on the surface so it can be absorbed to the root and die. You will typically need 2-3 days of nice weather w/ no rain so the stuff can be absorbed in and taken down to the root. I use a large sprayer on the p boat and drive around and target areas. (proper clothing and protection like covered skin, safety glasses and mask are strongly recommended...) Timing is the key when applying this approach. Work prevented me from hitting it at the best time this year and I only had marginal success...
http://www.lakerestoration.com/t-WaterLily-control.aspx
https://www.lakerestoration.com/product-finder.aspx
http://www.thepondguy.com/
http://www.thepondguy.com/category/pond-and-lake-aquatic-weed-control
Some of the aquatic herbicides can be used for vegetation control on land like weeds or poison ivy BUT I would be cautious of using land based weed killer on water type weeds.