World oceans are becoming more acidic as a consequence of CO2 anthropogenic emissions, with multiple physiological and ecological implications. So far, our understanding is mainly limited to some species through in vitro experimentation. In this study, we took advantage of a recent submarine eruption (from October 2011 to March 2012) at ~ 1 nautical mile offshore El Hierro Island (Canary Islands, central east Atlantic) to determine whether altered physical–chemical conditions, mainly sudden natural ocean acidification, affected the morphology, photosynthesis (in situ Chl-a fluorescence) and physiological performance (photo-protective mechanisms and oxidative stress) of the conspicuous brown seaweeds Padina pavonica—a species with carbonate deposition – and Lobophora variegata—a species without carbonate on thallus surfaces – , both with similar morphology. Seaweeds were sampled twice: November 2011 (eruptive phase with a pH drop of ca. 1.22 units relative to standard conditions) and March 2012 (post-eruptive phase with a pH of ca. 8.23), on two intertidal locations adjacent to the eruption and at a control location. P. pavonica showed decalcification and loss of photo-protective compounds and antioxidant activity at locations affected by the eruption, behaving as a sun-adapted species during lowered pH conditions. At the same time, L. variegata suffered a decrease in photo-protective compounds and antioxidant activity during the volcanic event, but its photosynthetic performance remained unaltered. These results reinforce the idea that calcareous seaweeds, as a whole, are more sensitive than non-calcareous seaweeds to alter their performance under scenarios of reduced pH.