Submarine emissions of gases from hydrothermal vents alter the surrounding chemical environment, influencing species responses to the resulting environmental gradients. The 2011 underwater eruption of the Tagoro volcano off the coast of El Hierro in the Atlantic Ocean changed the physical and chemical conditions, impacting the distribution of pelagic fauna. Post-eruptive stages from 2013 to 2018 revealed changes in both benthic and pelagic communities, with continuous eruptions further affecting local carbon cycle through shifts in nutrient concentrations and isotopic composition. The lowest δ13C values in zooplanktonic primary consumers were found in areas directly influenced by the Tagoro submarine volcano. Although the mixing model results show that phytoplankton is the primary carbon source for copepods, contributing an average of 28.3% of their carbon, magmatic CO2 and seawater dissolved inorganic carbon each account for approximately 17–18%. The isotopic signatures reveal a gradient of enrichment in copepods, reflecting the influence of inorganic nutrient and gas emissions from the volcano's centre to its periphery within the marine ecosystem. This data is useful for understanding the worldwide significance of environmental stressors such as volcanic eruptions on marine organisms.