Mollusk shells are abundant, persistent, ubiquitous physical structures in aquatic habitats. Using an ecosystem engineering perspective, we identify general roles of mollusk shell production in aquatic ecosystems. Shells are substrata for attachment of epibionts, provide refuges from predation, physical or physiological stress, and control transport of solutes and particles in the benthic environment. Changes in availability of these resources caused by shell production have important consequences for other organisms. Colonization of shelled habitat depends on individual shell traits and spatial arrangement of shells, which determine access of organisms to resources and the degree to which biotic or abiotic forces are modulated. Shell production will increase species richness at the landscape level if shells create resources that are not otherwise available and species are present that use these resources. Changes in the availability of resources caused by shells and the resulting effects on other organisms have both positive and negative feedbacks to these engineers. Positive feedbacks appear to be most frequently mediated by changes in resource availability, whereas negative feedbacks appear to be most frequently mediated by organisms. Given the diversity of species that depend upon resources controlled by shells and rapid changes in global shell production that are occurring due to human activities, we suggest that shell producers should not be neglected as a targets of conservation, restoration and habitat management.