We found evidence for a critical population bottleneck at a developmental-stage transition in larvae of the zebra mussel Dreissena polymorpha Pallas from field estimates of mortality. Identification of this critical period in the field was made possible by closely tracking cohorts of larvae over 5 days of development as they dispersed 128 km in a river system. The presence of a survival bottleneck during development was confirmed in laboratory studies of zebra mussel larvae. Development-specific mortality has important implications for spatial population dynamics of the zebra mussel in particular, and all species with indirect development in general. Marine reserves that do not take development-specific mortality into account may dramatically underestimate reserve size needed to protect rare and/or exploited marine populations. Conversely, for the zebra mussel, the lower contribution of dispersing individuals to population growth downstream of reserves can lead to more feasible control through the blocking of dispersal.