The expansion of global aquaculture has brought challenges from emerging pathogens, resulting in disease-related production losses across various regions. Among these pathogens, aquatic circoviruses—small, single-stranded DNA viruses initially detected in barbel (
Barbus barbus
)—have now been identified in multiple aquaculture species. These viruses have been associated with various clinical manifestations in economically important fish, crustacean, and mollusk species, including acute hemorrhage syndrome, which has shown mortality rates up to 95% in controlled laboratory infections of turbot. This review consolidates current knowledge on aquatic circoviruses, focusing on their genetic diversity, epidemiology, pathogenesis, and management strategies. The analysis encompasses observed host range patterns, documented instances of cross-species transmission, and evolutionary characteristics, such as host-specific clustering and recombination events. Research gaps are highlighted, particularly in understanding viral pathogenic mechanisms, host–pathogen interactions, and their ecological roles within aquatic ecosystems. We evaluate recent advances in diagnostic methods, including targeted vaccine design and RNA interference technology. The review outlines future research priorities, including elucidating cross-species transmission potential, developing effective treatments, and assessing the full economic impact of these viruses on aquaculture. By providing a comprehensive overview, this review aims to guide future research efforts and inform strategies to mitigate the impact of circoviruses on aquaculture sustainability.