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Dormancy is a common mechanism employed by short-lived organisms for persistence in a variable environment. Theory suggests that the fraction of propagules that terminate dormancy each year should be <100% when recruitment success varies temporally. Moreover, the fraction of propagules that resumes development should vary across habitats that differ in the probability of successful recruitment or the probability of survival during dormancy. We tested these predictions by using dormant eggs from five populations of the freshwater cladoceran Daphnia pulicaria that differ in their ability to recruit to and persist in the water column. In two separate experiments, newly produced dormant eggs were incubated in situ for one year at various sites on the bottom of the lakes. A series of reciprocal transplants among four of these populations separated the effects of lake-specific environmental cues from the genetic and maternal effects of the different populations. Additional eggs were incubated in the laboratory under photoperiod-temperature combinations representative of those in the field. We found that the annual hatching fraction ranged from 6% to 50% among lakes, and that hatching fraction was primarily driven by environmental cues rather than being a result of the source of the eggs. However, laboratory incubations demonstrated significant differences among populations in the trajectories of the hatching curves, and a much higher rate of hatching than the field incubations. Our results suggest that variation in dormancy strategies within these systems is likely influenced both by the seasonal risk experienced by the active individuals and by risks associated with entering the dormant egg bank.