Water sources are currently facing great challenges from rapid population growth and industrial developments. Investigations into how to remove algal organic matter (AOM) are thus of great importance from an environmental point of view because most lakes and reservoirs in South Korea suffer from algae problems, especially in the summer. Many efforts have been made to remove AOM from the aquatic environment in South Korea. In this study, we focus on development of a new AOM removal system, utilizing waste oyster shells and ferrihydrite as the media of the filtration system. Using this system, the removal rate of AOM was investigated regarding the concentrations of chlorophyll a, total phosphorus, and alginate. It was found that about 92% of the total phosphorus was removed through this system when raw oyster shell powders were heated at 900°C to convert them into calcium oxide powders. The use of a continuous system also led to a reduction of 94.2% in total phosphorus, 78.8% in chlorophyll a, and 43.6% in alginate.