Estuarine viral communities are highly sensitive to environmental gradients associated with freshwater–seawater mixing, seasonal variability, and anthropogenic disturbance. In subtropical estuarine ecosystems, these interacting drivers may reshape viral diversity, community composition, and virus–host interactions, yet their effects on seasonal viral succession remain poorly understood. Here, we investigated seasonal dynamics of DNA viral communities in two contrasting subtropical coastal habitats of Hong Kong: Deep Bay, a shallow estuarine bay strongly influenced by anthropogenic activities, and Tai Tan, a relatively pristine coastal site on the Sai Kung Peninsula. Seasonal water samples were analyzed using viral metagenomic sequencing to characterize major viral groups, including dsDNA phages, nucleocytoplasmic large DNA viruses (NCLDVs), and ssDNA viruses. We further assessed viral diversity, taxonomic composition, auxiliary metabolic genes (AMGs), and putative host associations, with particular emphasis on the roles of environmental variability and human disturbance in shaping viral community succession. This study provides new insight into how seasonal forcing and anthropogenic activities jointly structure viral communities in subtropical estuarine and coastal waters, and highlights the ecological importance of viruses in coastal ecosystem responses to environmental change.