As the population size of free-living European bison in Poland has increased significantly over the last few years, conservation and management should be reconsidered to face new challenges, which aim to protect the whole population, not just individuals. The aim of our study was to analyse prevalence and identify risk factors for infections with viruses affecting reproduction (BVDV, BoHV-1, and BoHV-4), causing respiratory diseases (BRV3, BAdV-3, and BRSV), and emerging vector-borne viruses (BTV and SBV). Over 600 serum samples used in serology and 270 lung tissue samples, and 284 nasal swabs used in virological tests were collected from 24 free-living and captive European bison herds between 2016 and 2023. The seroprevalences varied between low (0.3–6.1% for BVDV, BoHV-1, and BoHV-4), medium (15.9% for BRSV and 22.1% for BTV) and high (43.3% for BRV3, 59.5% for BAdV-3, and 69.5% for SBV). Interspecies’ and intraspecies’ risk of endemic viral infections was observed to be density-dependent, while the effect of anthropogenic factors on the spread of infections in free-living European bison has not been demonstrated. BTV is no longer circulating, while SBV has become endemic. The higher exposure to viruses in the European bison eliminated on the basis of a veterinary decision indicates the importance of an expert supervision for disease control and prevention.