Honey bees (Apis mellifera) are vulnerable to many diseases, including two species of the fungus Nosema, namely Nosema apis and Nosema ceranae. Nosema ceranae appears to be replacing Nosema apis, but its epidemiology, responses to drug treatments, climate, and wintering methods, and impact on colony productivity and survival are poorly understood. This study aimed to determine the seasonal pattern of Nosema abundance in two Alberta locations using indoor and outdoor wintering methods and the impact of Nosema on honey bee colony population and survival. This study also assessed the effects of spring and fall fumagillin treatment on spore abundance and colony productivity and mortality. Colonies that were naturally infected with Nosema had predominantly N. ceranae, but some had both N. ceranae and N. apis. Nosema ceranae had high spore abundance in spring, declining to low levels in the summer and fall. There was no clear pattern for differences in Nosema abundance between locations. Colonies that were wintered indoors had one-fifth the probability of mortality at similar Nosema abundance and more rapid spring population build-up than outdoor-wintered colonies. This suggests that the mitigation of temperature stress associated with indoor wintering reduced the impact of Nosema infections on colonies more than any potential benefits associated with late winter cleansing flights. Consequently, the existing Nosema threshold should be lower for outdoor-wintered colonies than those wintered indoors. Average Nosema abundance in the spring was a significant predictor of end-of-study winter colony mortality, highlighting the importance of spring Nosema monitoring and treatments. Fumagillin treatment in the spring and/or fall reduced Nosema abundance but did not eliminate the infection, making continued monitoring necessary. Honey bee colony population was improved by spring treatment, but not consistently between locations and years, possibly due to the late treatment application at a lower dosage than the label recommends. Previous spring and/or fall fumagillin treatment did not reduce spring Nosema abundance or increase colony population in the following spring. Therefore, to maintain low spring N. ceranae abundance, colonies should be treated in the spring even if treated in the previous fall. Treating with fumagillin in both the spring and fall increased colony survival in one of two years.