Marine zooplankton are central components of holistic ecosystem assessments due to their intermediary role in the food chain, linking the base of the food chain with higher trophic levels. As a result, these organisms incorporate the inherent properties and changes occurring atall levels of the marine ecosystem, temporally integrating signatures of physical and chemical conditions. For this reason, zooplankton-based biometrics are widely accepted as useful tools for assessing and monitoring the ecological health and integrity of aquatic systems. The European Marine Strategy Framework Directive (EU-MSFD) requires the use of different types of bio-monitors, including zooplankton, to monitor progress towards achieving specific environmental and water quality targets in EU. However, there is currently no comprehensive synthesis of zooplankton indices development, use, and associated challenges. We addressed this issue with a two-step approach. First, we formulated the indicator-metrics-indices cycle (IMIC) to redefine the closely related but often ambiguously utilized terms - indicator, metric and index, highlighting the convergence between them and the iterative nature of their interaction. Secondly, we formulated frameworks for synthesizing, presenting and systematically applying zooplankton indices based on the IMIC framework. The main benefits of the IMIC are twofold: 1). to disambiguate the key elements: indicators, metrics, and indices, revealing their links to an operational ecological indicator system, and 2) to serve as an organizing tool for the coherent classification of indices according to the MSFD descriptors. Using the IMIC framework, we identified and described two broad categories of indices namely the core biodiversity indices already in use in the Baltic Sea and North Atlantic regions, including the ‘Zooplankton Mean Size and Total Stock (zooplankton MSTS)’ and 'Plankton Lifeforms index (PLI)', and stressor-response indices retrieved from the existing literature, elucidating their applicability to different MSFD descriptors. Finally, major challenges of developing new indices and applying existing ones in the context of the MSFD were critically addressed and some solutions were proposed.