It's my understanding (subject to challenge) that a aeration system that is undersized has the potential to consistently pull toxic/DO void waters up into the upper water column where the fish live. If the system does not turn the waters over enough, the lower portions of the pond never detoxify/ and/or sufficiently hold DO and will continue to draft upwards creating a worse environment for the inhabitants above.

I suppose a small localized aeration system could do as Mike suggests and improve the muck in that area over time (physical disturbance would speed the process up - agreed), but I would venture to say that the over all health of the upper water column would suffer indefinitely given that the system was not capable of turning the water over enough.

Dredging might be a more appropriate localized effort, but big money comes back into play.

I am certainly open to a lesson from those with the experience that I lack.

Fish on!,
Noel