In an era of rapid industrialization, the discharge of contaminated effluent into natural environments has significantly increased with a direct, negative impact on aquatic biodiversity. It is not only discharged industrial effluent, but also products discharged from wastewater treatment plants, that disrupt biogeochemical cycles, which have direct relationships with aquatic biodiversity. Due to this situation, microbial biodiversity is also affected. Microbial wastewater treatment is a sustainable way to protect aquatic biodiversity, for which environmental microbiome conservation is very important. This article explores the delicate topic of biodiversity conservation, specifically aquatic biodiversity conservation, and is aimed at improving and informing aquatic biodiversity policies.