To minimize muck on pond bottoms the best way to do it is to reduce the eutrophication and nutrient inputs of the pond more toward oligotrophic conditions with low organic inputs such as leaves and very clean water (only roof water) or minimal water from the water shed. Pond muck comes from dead organics that have grown, blown or washed into the pond. Ideally invertebrates, a few vertebrates, and bacteria temporarily bind and/or process that muck into the basic nutrients that feed the pond plant community. Nutrient cycling. Lots of nutrients results in lots or excess plant growth and some animals that when dead, results in muck. Reduce the nutrients and it reduces the annual accumulation of muck. Lack of oxygen on top of the sediments results in anaerobic conditions which is a much slower form of decay of dead organics, thus the muck can accumulate faster than it can be decayed or processed. Excess chemical additions can often suppress the bacterial decay - recycling processes.
