Sturgeon mimiviruses can cause a lethal disease of the integumentary systems of sturgeon (Acipenseridae). Here we provide phylogeographic evidence that sturgeon mimivirus is endemic in endangered populations of wild Lake Sturgeon within Canada's Hudson Bay drainage basin. Namao virus (NV) variants were diagnosed in 24% of Lake Sturgeon samples (n = 1329) collected between 2010-2015. Lake Sturgeon populations with the highest virus prevalence were from the Nelson River (58%) in 2015, Saskatchewan River (41%) in 2010 and South Saskatchewan River (36%) in 2011. Bayesian phylogenetic reconstructions suggested that four NV variants, designated HBDB I-IV, co-circulate temporally and spatially within and between the genetically and biogeographically distinct Lake Sturgeon populations. Evidence from recapture studies suggested that Lake Sturgeon across the basin are persistently infected with NV at prevalence and titer (103.6 equivalent plasmid copies per µg DNA) levels consistent with the hypothesis that wild Lake Sturgeon populations serve as a maintenance population and reservoir for sturgeon mimiviruses. Bayesian hierarchical modeling of NV in the Landing River population of Lake Sturgeon suggested that host weight and age were the best predictors of sturgeon mimivirus presence and titer, respectively, whereas water flow rate, level and temperature, and number of previous captures did not significantly improve model fit. A negative relationship was estimated between sturgeon mimivirus presence and Lake Sturgeon weight and between virus titer and Lake Sturgeon age.