Free‐living red coralline algae play an important role in the carbon and carbonate cycles of coastal environments. In this study, we examined the physiology of free‐living coralline algae forming maerl beds in the Bay of Brest (Brittany, France), where Lithothamnion corallioides is the dominant maerl (i.e., rhodolith) species. Phymatolithon calcareum and Lithophyllum incrustans are also present (in lower abundances) at a specific site in the bay. We aimed to assess how maerl physiology is affected by seasonality and/or local environmental variations at the inter‐ and intraspecific levels. Physiological measurements (respiration, photosynthetic and calcification rates) were performed using incubation chambers in winter and summer to compare (1) the dominant maerl species at three sites and (2) three co‐existing maerl species at one site. Comparison of the three co‐existing maerl species suggests that L. corallioides is the best adapted to the current environmental conditions in the Bay of Brest, because this species is the most robust to dissolution in the dark in winter and has the highest calcification efficiency in the light. Comparisons of L. corallioides metabolic rates between stations showed that morphological variations within this species are the main factor affecting its photosynthetic and calcification rates. Environmental factors such as freshwater inputs also affect its calcification rates in the dark. In addition to interspecies variation in maerl physiology, there were intraspecific variations associated with direct (water physico‐chemistry) or indirect (morphology) local environmental conditions. This study demonstrates the plasticity of maerl physiology in response to environmental changes, which is fundamental for maerl persistence.