CS normally (when used in proper methods and amounts) only kills green plants. It can kill some fish species as it inhibits gill/air exchange function in low alkalinity water. It can accumulate over time in pond bottom soil which can be an issue.

Manual removal of FA is a much better (but back breaking) alternative. Hydrated lime in limited amounts can kill FA (only a spot check method) not for large portions of the pond).

I highly recommend that you id the FA or problem plants before any treatment.