The implementation of directives such as the European Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD) has promoted the development of several tools and methods for assessing the ecological health of marine ecosystems. Within the scope of the WFD and in terms of rocky shores, several multimetric tools were developed based on the macroalgae biological quality element (BQE), in addition to those based on macroinvertebrates. The WFD requires member states to assess each BQE separately. The present work aimed to test the ability of ecological indices to distinguish sites within anthropogenic disturbance gradients caused by organic enrichment, using macroinvertebrate communities on intertidal rocky shores. Owing to the lack of more specific indices (for rocky shore), indices based on abundance, diversity and/or taxonomic composition were selected from several widely used indices in ecological studies and/or developed for soft-bottom macroinvertebrate communities. Present findings reveal several indices based on diversity and/or taxonomic composition able to distinguish sites within the disturbance gradients, showing increasing quality from the site nearest the source of organic enrichment to that farthest from it, especially indices calculated using biomass data, and in the summer season. Such results open good perspectives for the use of intertidal macroinvertebrate communities from rocky shores, and also help add the perspective of this biological quality element in the ecological quality assessment of coastal waters.