Estuaries and lagoons are especially affected by anthropogenic pressures. This has resulted in symptoms of degradation including water quality impairment and loss of aquatic biota. Protection of aquatic biodiversity and management of these coastal systems require robust tools to assess habitat integrity. Fish populations have been extensively used to define habitat integrity in freshwater systems. Comparatively much less has been achieved in estuarine, lagoonal and related coastal systems classified as transitional systems under the European Water Framework Directive (WFD). The implementation of the WFD has prompted the rapid development of estuarine fish indices across Europe. In this context, this paper reviews seventeen published fish-based indices applied to estuarine systems worldwide and summarises common development strategies. Most indices are computed from a number of independent metrics and are based on assemblage composition or functional attributes of fish species (guilds). Among metric groups, species richness–composition metrics are the most widely used in current indices, followed by habitat guild, trophic guild, abundance and condition, and finally nursery function metrics. Within these, indicator species or guilds associated with estuarine quality features often dominate the indices. Development strategies vary but generally include (1) selection and calibration of metrics to anthropogenic pressure; (2) development of reference conditions; (3) comparison of metric values to reference ones; and (4) designation of thresholds for ecological status class. All index developers invest a large amount of effort on the definition and formulation of the reference values. Comparatively less effort is invested in the evaluation of the relevance and precision of the assessment. Only about half of the indices reviewed attempt any validation of the index outcomes and these are limited to simple correlation analysis and misclassification rate analysis by comparing index value with anthropogenic pressure proxies. Currently there are no uropean-wide consistent fish indices for transitional waters. Widening of the geographical relevance will require better precision in the formulation of reference conditions and greater inclusion of functional attributes in the indices. More recent transitional fish indices have paid increased attention to sampling method and effort, as well as metric sensitivity and robustness. This trend has continued parallel to the implementation of WFD-monitoring programmes across Europe. Further improvements are still needed to link pressures with index response and the characterisation of uncertainty levels in the index outcomes.