The aim of this study was an assessment of the prevalence of human enteric viruses such as norovirus (NoV) and hepatitis A and E virus (HAV, HEV) in mussels sold on the Polish market. In addition, the presence of human (hAdV) and swine (pAdV) adenoviruses as indicators of faecal contamination of shellfish was also studied. In total, 246 shellfish samples representing 41 batches of blue and Mediterranean mussels were purchased from Polish seafood wholesalers. Shellfish were processed according to the method in ISO 15216-2:2019 followed by isolation of viral nucleic acids using NucliSens®Magnetic Extraction Reagents (bioMérieux). For virus detection several duplex real-time PCR protocols with incorporated internal amplification controls (IAC) were used. The presence of human enteric viruses was shown in 42 shellfish samples (17.1%). The most frequently detected were NoV (41 samples; 16.7%) followed by HEV (1 sample; 0.4%). None of the samples was positive for HAV, hAdV or pAdV. 15 shellfish batches (36.6%) were virus positive. By the use of Bayesian inference, a true seasonal and country related virus prevalence in shellfish was estimated. NoV GI was more frequently detected in Dutch mussels (18.9%; 95% CI: 6.7%–34.0%), while NoV GII was more frequent in Danish mussels (17.1%; 95% CI: 5.8%–32.5%). However significant differences in virus prevalence in individual and shellfish batches between producing countries were not shown. A seasonal virus distribution pattern in shellfish samples was observed. Lower level of NoV contamination was found in mussels harvested during spring-summer (0.0%–1.3%, 95% CI: 0.1%–4.8%) compared to the fall-winter season (13.0%–20.7%, 95% CI: 6.1%–31.2%). For shellfish batches, a similar seasonal correlation was only observed for NoV GII. The monitoring of marketed shellfish would be an essential tool allowing a reduction of the number of viral food-borne outbreaks.