Submarine volcanic activity releases large amounts of gases and metals in the water column, affecting biogeochemical cycles and ecosystems at a regional and local scale. In 2018, Fani Maoré submarine volcano erupted 50 km offshore Mayotte Island (Comoros Archipelago, Indian Ocean). Active eruptive plumes were observed in May 2019 at and around the summit with acoustic plumes rising 2 km into the water column coupled to strong geochemical anomalies. Between May 2019 and October 2020, three research cruises monitored the eruptive activity. Here, we report spatial and temporal variability of water column chemistry above the volcano, focusing on dissolved gases, trace metal concentrations, and physico-chemical parameters. In May 2019, concentrations above 800 nM in CH4 and H2 were measured throughout the water column, with Total Dissolvable Mn and Total Dissolvable Fe concentrations above 500 nM, and CO2 values of 265 μM. Strong water column acidification was measured (0.6 pH unit) compared to the regional background. From May 2019 to October 2020, we observed a general decrease in gas concentrations, and an evolution of the TDMn/TDFe ratios similar to previously reported values in other submarine volcanic contexts, and consistent with a decrease of the eruptive activity at the volcano. In October 2020, a rebound of high H2 concentrations resulted from new lava flows, which were identified by seafloor observation using deep-towed camera, 5 km further than the volcano summit. During 2 years timespan of our observations (2019–2020), He, CO2 and CH4 concentrations correlate highlighting a magmatic origin of dissolved gases. δ13C-CH4 values of −34‰ vs. vPDB might suggest magma/sediments interaction during the magma ascent, and potential thermal cracking of organic matter, although abiotic methane generation cannot be ruled out given the volcanic context. Weak correlations between H2 and excess of 3He suggest complex processes of H2 from magmatic degassing, lava/seawater interaction, and oxidation processes in the water column. Strong and correlated Fe, Mn and Si water column anomalies are also consistent with fluid-rock reactions induced by acidic fluids rich in magmatic volatiles. Water column acidification appears to be associated with the release of CO2-rich fluids. A year after the main eruptive event, the system seems to be back to steady-state highlighting the buffer capacity and resilience of the seawater column environment.