Abstract Background and Aims Maerl-associated communities have received considerable attention due to their uniqueness, biodiversity and functional importance. Although the impacts of human activities are well documented for maerl-associated macrofauna, the spatio-temporal variations of macroalgae have comparatively been neglected, and the drivers that influence their dynamics are poorly known. We investigate the links between maerl-associated macroalgal communities, anthropogenic pressures and environmental conditions, and hypothesize that sites under human pressure would exhibit different dynamics when compared to reference site. Methods In order to better understand community variation through space and time, four subtidal maerl beds under different pressures were consistently monitored over one year in the bay of Brest, Brittany, France. Both macroalgae communities monitoring and environmental data were acquired through field sampling and available models. Key Results Higher macroalgal biomass was observed within eutrophic sites, especially in summer (more than 10 times higher than in Unimpacted site), caused by free-living forms of opportunistic red macroalgae. The Dredged site also exhibited distinct macroalgal communities during summer from the Unimpacted site. Nutrient concentrations and seasonality proved to be key factors affecting the macroalgal community composition, although dredging and its effects on granulometry also had strong influence. Over the long term, less than half of the species identified during historical surveys were found, indicating major temporal changes. Conclusions Human pressures have strong impact on maerl-associated macroalgal communities. Nutrient concentrations and dredging pressure appear as the main anthropogenic factors shaping maerl-associated macroalgal communities. Additionally, our results suggest historical changes in maerl-associated macroalgal communities over 25 years in response to changes in local human pressure management. This study suggests that maerl-associated macroalgal communities could be used as indicators of anthropogenic-driven changes in this habitat.