Wetland soils contain a reservoir of dormant plant seeds and invertebrate eggs, collectively termed the seed or propagule bank, which integrate spatiotemporal variation at various levels of biology (genetic, phenotypic, species, and community). Several recent studies suggest that anthropogenic physical or chemical stressors may disrupt the process of emergence from propagule banks. This process is often the single most important colonization process in wetlands isolated geographically from other water bodies. The potential for disruption of emergence can be exploited as a useful indicator of anthropogenic stress. The aim of our paper is to provide a conceptual framework that shows the advantages and limitations of wetland propagule banks as indicators of anthropogenic stress or ecological integrity. This framework describes mechanistic responses of propagule banks to stressors and makes recommendations on experimental approaches for the evaluation of cause–effect relationships between stressors and propagule bank responses. This indicator could help bridge the current gap between basic and applied wetland ecology and could find application in future wetland management and restoration strategies.