Pond Boss Forums AQUATIC VEGETATION Controlling unwanted plants What to do about Brittle Naiad?

There are many variables involved in the answer to your question. But in general; yes, you should apply directly to the infested areas - knowing fully well that the active-ingredient will likely diffuse or disperse into the adjacent untreated areas to some degree or another.
I would suggest having a conversation your chemical supplier for specific details and use-rate recommendations - after you've described the pond's various perameters and its level of infestation.