Muskrat (Ondatra zibethicus) populations show long-term and widespread declines across North America, necessitating research into potential mechanistic explanations, including population health. Previous research established reference hematology values, a proxy of individual health, of muskrats occurring in highly modified ecosystems. However, our knowledge of hematology metrics in muskrat populations occurring in more natural ecosystems is limited. We measured several hematological parameters of wild-caught muskrats (n = 73) in the Greater Voyageurs Ecosystem in northern Minnesota in 2018–2019 to establish baseline muskrat health in a relatively intact, near-pristine ecosystem. Additionally, we measured rectal temperature and heart and respiratory rates and collected whole blood for complete blood cell count assessment. We established baseline physiologic and hematologic reference ranges for the population and describe variations between total white blood cells, nucleated cell differentials, and basic erythron and platelet estimates and demonstrate methods of estimation to be poor proxies for more standardized counting methods. Our results establish a baseline to compare muskrat health assessments for populations affected by landscape change or in decline.