China has the world’s largest industry of fishing and aquaculture (defined here as “fishery”). China is the world’s largest producer, consumer, processor, and exporter of aquatic products, with a production of >68 million tonnes in 2022. China alone contributes more than 60% of global aquaculture volume. Aquaculture accounts for 80% of domestic fish production in China. Fishery industry plays an important role in ensuring national food security and nutritional security, particularly, in meeting the demand of high-quality protein. Whereas, with the fast expanding of aquaculture in the last three decades in both inland and coastal waters, the ecological effects of aquaculture, i.e., the possible impacts of aquaculture on the environments of aquaculture waters and its adjacent waters are receiving widespread attention from a variety of stakeholders. The discipline of fishery ecology and environment focuses on the interactions of aquaculture and environments, particularly the impacts of fisheries activities on natural water ecosystems, as well as the impacts of climate change and human activities on sustainable production of aquatic products, and their influences on ecological and environmental characteristics of fishery waters. Also, it focuses on the scientific theories and technologies of bio-remediation and restoration of degraded fishery habitats and aquatic ecosystems. Here, we summarized the main progresses made in this discipline in the past ten years and proposed the key points which should be paid attention to or further investigated in the future. Our aim is to provide an overview on the current status of ecological and environmental characteristics of fishery waters and draw more attention from both scientists and public on related research.