Metatranscriptomic (i.e., total RNA) sequencing of fish over the past decade has led to the discovery and characterisation of a vast diversity of fish-associated viruses. While these cross-sectional studies provide insights into species level virome diversity at a single time point, because of the more laborious sampling required there is a marked absence of longitudinal studies that examine how fish viromes change through time. We examined tissue samples from three species of common market fish – Girella tricuspidata (Black bream), Mugil cephalus (Flathead grey mullet) and Sillago flindersi (Eastern school whiting) – collected monthly over the period of a year from the Sydney Fish Market (Sydney, NSW, Australia). Gill, liver and spleen tissue from 352 individuals were pooled into 25 sequencing libraries based on species and time of collection. Metatranscriptomic sequencing of these samples revealed viruses from 30 viral families including likely fish-infecting candidates in the vertebrate-associated families Astroviridae, Caliciviridae, Chuviridae, Coronaviridae, Hantaviridae, Hepadnaviridae, Hepeviridae, Matonaviridae, Picornaviridae, and the order Reovirales. Viruses from the Picornaviridae were particularly commonplace and a diversity of Hepadnaviridae were observed. Notably, viruses from each species of fish formed distinct clades suggesting a lack of virus cross-species transmission. Additionally, we observed a continual turnover of viruses within these fish, reflecting their transient presence in populations, and no discernible patterns in viral abundance and diversity.