Ballast water has been identified as a leading vector for introduction of non-indigenous species. Recently, the International Maritime Organization implemented management standards—D-2—where all large, commercial ships trading internationally are required to adopt an approved treatment system using technologies such as ultraviolet radiation or chlorination. However, current management regulations are based only on the total abundance of viable taxa transported (i.e. total propagule pressure), largely ignoring species richness (i.e. colonization pressure). To determine the efficacy of chlorine treatment in reducing invasion risks and changes in transported biological communities inside ballast tanks, we used DNA metabarcoding-based approaches to estimate colonization pressure (here, the number of species/operational taxonomic units [OTUs] introduced) and relative propagule pressure (relative abundance of each species/OTU) of zooplankton communities in control and chlorine treated tanks during four transatlantic voyages. Our study demonstrated that transport itself did not significantly reduce colonization pressure of zooplankton species, nor did chlorine treatment. Chlorine treatment altered community structure by reducing relative propagule pressure of some taxa such as Mollusca and Rotifera, while increasing relative propagule pressure of some Oligohymenophorea and Copepoda species. Synthesis and applications. Chlorine treatment may not reduce invasion risks as much as previously thought. Reduction in total propagule pressure does not mean reduction in abundance of all species equally. While some taxa might experience drastically reduced abundance, others might not change at all or increase due to hatching from dormant stages initiated by chlorine exposure. Therefore, management strategies should consider changes in total propagule pressure and colonization pressure when forecasting risk of new invasions. We therefore recommend adopting new approaches, such as DNA metabarcoding-based methods, to assess the whole biodiversity discharged from ballast water. As species responses to chlorine treatment are variable and affected by concentration, we also recommend a combination of different technologies to reduce introduction risks of aquatic organisms. Fil: Lin, Yaping. Geomar-Helmholtz Centre for Ocean Research Kiel; Alemania Fil: Zhan, Aibin. Chinese Academy of Sciences; República de China Fil: Hernández, Marco R.. University of Windsor. Great Lakes Institute for Enviromental Research; Canadá Fil: Paolucci, Esteban Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina Fil: MacIsaac, Hugh J.. University of Windsor. Great Lakes Institute for Enviromental Research; Canadá Fil: Briski, Elizabeta. Geomar-Helmholtz Centre for Ocean Research Kiel; Alemania