The European honey bee species (Apis mellifera L.) is under increasing pressure from anthropogenic and other stressors. Winter mortality of entire colonies is generally attributed to biological, environmental, and management conditions. The rates of winter mortality can vary extremely from place to place. A landscape approach is used here to examine the dependency between spatially distributed winter mortality rates, environmental and biological conditions, and apiary management. The analysis was applied to data for the region of Wallonia in Belgium with winter mortality rates obtained from the European project EPILOBEE. Potential explanatory variables were spatially allocated based on GIS analysis, and subjected to binomial linear regression to identify the most predominant variables related to bee winter mortality. The results point to infestation with Varroa, the number of frost days, the potential flying hours, the connectivity of the natural landscape, and the use of plant protection products as most dominant causes for the region of Wallonia. The outcomes of this study will help focus beekeeping and environmental management to improve bee health and the effectiveness of apiary practices. The approach surpasses application to the problem of bee mortality and could be used to compare and rank the causes of other environmental problems by their significance, particularly when these are interdependent and spatially differentiated.