Abstract: Aquatic viruses are viruses that infect various aquatic organisms or exist in different aquatic systems. They are the most abundant biological entities in aquatic ecosystems and significantly affect the structure and function of host communities, thereby influencing the biosphere and global biogeochemical cycles. Whether from the perspective of taxonomic status, host range, genetic evolution, or ecological effects, aquatic viruses exhibit highly diversity and cross-domain characteristics. Previous understanding of viral infection and its impact has been mainly focused on the interaction between viruses and host cells and at the molecular level. However, to clearly understand the role of aquatic viruses in ecosystems and their influence on biogeochemical cycles, it is essential to employ a multi-scale approach from microscopic, mesoscopic, and macroscopic scales, leveraging remote sensoscopic and cutting-edge technologies for observation. This article provides an overview of the latest research progresses on cross-domain aquatic viruses and characteristics, driving species evolution, virus shunt and geochemical cycle effects, as well as related emerging technologies.