An index CCO (cover, characteristic species, opportunistic species) has been developed for the implementation of the European Water Framework Directory (WFD) in coastal waters, using intertidal macroalgal communities as bio-indicator (Biological Quality Element). CCO is based on the calculation of three metrics corresponding to the global cover of macroalgal communities (metric 1), the number of characteristic species per topographic level/seaweed community (metric 2) and the cover of opportunistic species (metric 3). The final rating is obtained by pooling the scores of the three metrics. Results are given for 32 sites in 29 water bodies, grouped into four biogeographic regions along the Channel–Atlantic coasts of France. Over the six-year study, most of sites were sampled twice each (every three years). CCO index revealed that 25 coastal water bodies of both the Channel and the Bay of Biscay were in good or high ecological quality status (EQS), whereas only 4 of them were moderate and none in poor to bad status. However, significant differences have been found between sites and between geographic regions, water bodies located in Brittany obtaining the best EQS. No significant change occurred between the three-year sampling sets. A significant correlation has been established between a three-component anthropogenic pressure index and CCO ratings, showing the accuracy of CCO to evaluate the impact of anthropic activities on the structure and development of macroalgal communities as indicator of the ecological quality of coastal water bodies.