Background: Taenia taeniaeformis and the related zoonotic cestode Echinococcus multilocularis both infect the water vole Arvicola terrestris. We investigated the effect of age, spatio-temporal and season-related factors on the prevalence of these parasites in their shared intermediate host. The absolute age of the voles was calculated based on their eye lens weights, and we included the mean day temperature and mean precipitation experienced by each individual as independent factors. Results: Overall prevalences of E. multilocularis and T. taeniaeformis were 15.1% and 23.4%, respectively, in 856 A. terrestris trapped in the canton Zürich, Switzerland. Prevalences were lower in young (≤ 3 months: E. multilocularis 7.6%, T. taeniaeformis 17.9%) than in older animals (>7 months: 32.6% and 34.8%). Only 12 of 129 E. multilocularis-infected voles harboured protoscoleces. Similar proportions of animals with several strobilocerci were found in T. taeniaeformis infected voles of <5 months and ≥5 months of age (12.8% and 11.9%). Multivariate analyses revealed strong spatio-temporal variations in prevalences of E. multilocularis. In one trapping area, prevalences varied on an exceptional high level of 40.6-78.5% during the whole study period. Low temperatures significantly correlated with the infection rate whereas precipitation was of lower importance. Significant spatial variations in prevalences were also identified for Taenia taeniaeformis. Although the trapping period and the meteorological factors temperature and precipitation were included in the best models for explaining the infection risk, their effects were not significant for this parasite. Conclusions: Our results demonstrate that, besides temporal and spatial factors, low temperatures contribute to the risk of infection with E. multilocularis. This suggests that the enhanced survival of E. multilocularis eggs under cold weather conditions determines the level of infection pressure on the intermediate hosts and possibly also the infection risk for human alveolar echincoccosis (AE). Therefore, interventions against the zoonotic cestode E. multilocularis by deworming foxes may be most efficient if conducted just before and during winter.