A myxozoan parasite, Myxobolus inornatus, is one disease agent identified in young of the year (YOY) smallmouth bass in the Susquehanna River Basin, Pennsylvania. We investigated spatial and temporal variability in M. Inornatus prevalence across the Susquehanna River Basin and at several out-of-basin sites. We examined potential land use drivers of M. Inornatus prevalence including agricultural and developed land use. In 1,267 YOY smallmouth bass collected from 32 sites during 2013–2016, M. Inornatus was documented in 43.6% of samples. Among-site variability in parasite prevalence was greater than among-year variability. The effect of agricultural land use on M. Inornatus prevalence had a high probability of being positively correlated at multiple spatial scales (probability of positive effect > 0.80). The effect of developed land use on M. Inornatus prevalence had a relatively high probability of being negatively correlated at multiple spatial scales (probability of negative effect > 0.70). Our results suggest that land use practices could be related to M. Inornatus infection of smallmouth bass. Further study will be necessary to determine whether disease dynamics are a consequence of effects on the host, alterations of instream habitat mediating invertebrate host dynamics and/or survival and dispersal of the parasite infective stage.