The construction of dams and reservoirs has profoundly altered the natural flow regimes of nearly two-thirds of the world‘s major rivers exceeding 1000 kilometers in length. With more than 90000 reservoirs, China ranks first in the world for the number of reservoirs. A series of complex factors, including the dam‘s trapping effect, hydraulic scheduling, local hydrometeorology, sediment inputs etc., not only shape reservoir sediments as a unique habitat, but also influence the diversity and functionality of microbial communities in the sediments. Microorganisms are the fundamental drivers of material cycling in the aquatic environment system and have important influences on the structure of watershed ecosystem, biogeochemical cycling of elements, global climate change, etc. Reservoirs alter sediment microbial communities not only via the changes of a variety of physical, chemical, and biological conditions, but also by dynamically influencing the spatiotemporal distribution of environmental-ecological conditions. In response, microbial communities in sediment also react by altering surrounding environmental conditions to some extent. Existing studies on individual factors, although relatively complete, lack systematicity, which hinders further in-depth understanding of the important interactions between microorganisms and hydraulic and ecological environment. Therefore, 189 related research articles have been collected and analyzed by 7th May, 2025, and this article reviews the physical, chemical, ecological impacts of reservoirs on sediment microbial communities, classifies and summarizes a series of responses of sediment microbial communities under hydrological regulation, and summarizes the environmental and ecological impacts brought by microbial communities. Results show that most of the existing studies consider reservoirs as lake-like habitats, and few studies consider changes in hydraulic conditions or special characteristics of the habitat; Although there are studies targeting microorganisms in sediments of water reservoirs, they are more focused on the biogeographical distribution patterns and less on the interactions between environment and microbial communities. Faced with the deficiencies in current research, it is recommended to strengthen the integration of interdisciplinary fields and to carry out in-depth related research in the fields of ecological and environmental effects of microbial communities, application of microbial ecology techniques and theories, development of big data and artificial intelligence models, global climate change and greenhouse gas emission reduction, etc.