Morphological or behavioral defense mechanisms are important evolutionary strategies for the survival of prey. Studies have focused on predation and competition, but infection has been overlooked, despite being a determining factor of distribution and species diversity of prey. We hypothesized that the winter migration of Daphnia pulicaria is a community defense strategy to avoid fungal infection. To test this hypothesis, environmental variables and the Cladocera community, including D. pulicaria, were monitored in three study sections of the Anri Reservoir in the Republic of Korea during September 2010–August 2015. During three winter seasons, the density of infected D. pulicaria increased in all study sections, and they migrated from the central to the littoral area. Most of the infected individuals had dormant eggs in sexually reproducing mothers. However, when the proportion of non-infected individuals was higher than that of infected individuals, winter migration was not observed. Additional microcosm experiments showed that dormant eggs of D. pulicaria obtained from ice crystals in the littoral area had lower hatching and infection rates than those obtained from mothers moving from other zones. Therefore, the migration of D. pulicaria during winter is an active response to avoid intergenerational fungal infection.