The increasing degradation of marine ecosystems as a result of increasing impact caused by anthropogenic pressures, urges for well-founded knowledge to develop efficient tools to appraise the quality status of fish assemblages, as required by the “Marine Strategy Framework Directive”. This study analyzed the structural and functional response of rocky fish assemblages to several pressures on the Portuguese coast, i.e. fishing, sewage discharges, port activities and thermal effluent, by selecting fish-based metrics that best distinguished disturbed from control areas. One of the novel aspects of this research is the integrated assessment made through the analysis of several metrics representing numerous attributes of fish assemblages (namely diversity, abundance, trophic structure, mobility, resilience, habitat association, nursery function), which contrasts with the most commonly used approaches that in general focus on fish species/families. PERMANOVA results showed significant differences on metrics composition for all pressures with the exception of the thermal effluent. Moreover, two major patterns of stress were identified: (1) selective pressure, which affects differentially the fish assemblages (fishing); (2) broad-range pressure, which affects the entire fish assemblage with metrics of several attributes (e.g. structure, resilience, trophic guilds, nursery function) responding to its presence (sewage discharges, port activities). Taking into account the sensitivity results (discriminant analysis and Mann–Whitney test), biological meaning and redundancy with other metrics (Spearman correlations), the following metrics were selected as the most suitable to detect changes on temperate reef fish assemblages: “density of generalist individuals”, “density of territorial individuals”, “density of large individuals with medium to high commercial value (>20cm)”, “density of juveniles” and metrics relative to trophic guild (except zooplanktivores). Since metrics grouped species that have some degree of functional overlap, the present approach was useful to understand human-induced changes at the assemblage level, contributing for the future use of marine fishes as biological indicators.