The large global generation and improper management of waste lead to the pollution of the environment and efforts toward reducing the impacts of anthropogenic activities on aquatic environments should be prioritized. The United Nations declared 2018-2028 as the international decade for action on “Water for Sustainable Development” and integrated management of water resources. Several international initiatives, such as the UN 2030 Agenda, the Sendai Framework for Disaster Risk Reduction and the Paris Agreement, have highlighted and strongly recommended the development of new technologies to reverse the current environmental scenario of global water bodies. The use of anaerobic digestion for treating organic wastes can minimize and avoid several adverse effects on aquatic environments while promoting nutrient cycling and the production of biogas, a renewable energy source that can replace fossil fuels and therefore decrease the emission of greenhouse gases. We performed a systematic review to evaluate the contribution of anaerobic digestion in preventing and reducing human impacts on aquatic ecosystems. China (15.1%), Spain (7.3%) and Italy (7.3%) are countries with a pronounced research focus on this topic, indicating their awareness on the importance of managing and preserving their water resources. The integration of co-digestion and pretreatment methods into anaerobic digestion improved the production of byproducts (especially energy and biofertilizer). Thus, this review highlights the success of AD technology as a waste treatment strategy, while reducing the damage inflicted to aquatic systems and its consequences to human health and aquatic biodiversity.