Isolating a treatment area may provide advantages from a herbicide-performance standpoint; but certainly isn't the best option if fish (and low dissolved oxygen levels) are a concern.
Instead, I'd suggest using the AQUATHOL to treat the semi-isolated area WITHOUT trapping the fish within that area. Presuming that moderate circulation exists throughout the pond, the vegetation within the larger untreated area may help to partially offset the 02 demand from the decomposing plants that were controlled within the treatment area.
