Pelleted lime and gyp have a binder that is brown but it dissipates quickly. My guess is the brown is plankton that the lime and gyp had little effect on but the chlorine killed. Vinegar is not near as strong as bleach. Chlorine can bind with the soil and cause long term problems with fish and plankton. Did you notice if there was any settling in the bottom of the bucket? If it is indeed plankton/organics then an option would be a copper product . Chleated copper products don't cause soil problems. With no organics there will be no food chain to support a fish population absent feeding.

Here is one example http://plants.ifas.ufl.edu/guide/cutrine_label.pdf

With no soil to impact CUSO4 copper sulfate could be an option.

I doubt Alum would help in reasonable amounts as it does not sound like a suspended soil problem.