The assessment and preservation of the marine environment, particularly coastal ecosystems, has emerged as a global priority. In this study, the rocky bottom quality (CFR) index, which is based on macroalgae composition and abundance, was used to assess the ecological quality of coastal waters at six sites along the Algerian coast that represent a wide range of anthropogenic pressures. The sensitivity of the CFR index to the anthropogenic pressure index (MALUSI) was also assessed. Multivariate analyses (DCA, nMDS, cluster, SIMPER, and PCA) were used to assess the variability of macroalgal community structure. The CFR index calculated for this study was compared to the EEI-c and CARLIT indices. The CFR index classified the study sites based on ecological quality: good to high quality in the western sites (Ténès, Kouali1, and Kouali2) and moderate quality in the central sites (Fontaine, Fort de l’eau, and Surcouf). The findings indicate that the CFR and MALUSI indices are highly correlated. The abundance and composition of macroalgal communities are useful indicators of rocky shore quality, as demonstrated by structural analyses of characteristic macroalgae and opportunistic species. The competitive characteristic macroalgae of the Cystoseira sensu lato species were found to be associated with sites of good and high ecological quality. Stress-tolerant characteristic macroalgae (Pachymeniopsis lanceolata, Ellisolandia elongata, and Halopteris scoparia) and opportunistic ruderal species (Ulva rigida, Ulva lactuca, and Ulva linza) were found in sites with moderate ecological quality. The CFR index was compared with the EEI-c and CARLIT indices, and it can be noted that the three indices use different spatial scales, biological levels and species classifications. Therefore, CFR, EEI-c, and CARLIT indices are useful tools for assessing the quality of coastal waters.