ABSTRACT Knowledge of viral infection in marine mammals, a group severely threatened by human activity, is largely limited to the pathology and epidemiology of few endemic viruses. The recent emergence in marine mammals of high‐consequence viruses, such as H5N1 avian influenza and rabies, underscores the importance of understanding the ecology of viral transmission in these species. Metatranscriptomic approaches now enable relatively unbiased characterisation of full viral communities that can reveal ecological and evolutionary drivers of infection. We sequenced RNA from 15 marine mammal species (42 pools, 237 tissues, 128 animals) sampled in Scotland through the Scottish Marine Animal Strandings Scheme. Viral sequences were detected in 41 of 42 pools, representing more than 120 distinct viral taxonomic units (vOTUs). Virus host network analysis showed that viral communities were partly structured by host taxonomy, with clear differences between seals and cetaceans. However, vOTUs were frequently shared between species, mirroring reported ecological interactions, including cross‐order sharing between seals and cetaceans. Generalised linear models showed no effect of host taxonomy on viral richness. Instead, age was the strongest predictor: juvenile pools contained roughly twice as many viral taxa as adults and more than neonates, indicating that changing population demography may impact viral transmission in marine mammals. These results provide a basis for understanding how anthropogenic stressors may exacerbate viral transmission in marine mammals and demonstrate the increasing practicality of using genomics to understand ecological and evolutionary drivers of virus infection in natural populations.