This study provides the first comprehensive analysis of the nasal microbiota (NM) in two marine fish species, the European sea bass and the Atlantic cod. Given its direct environmental exposure, fish NM is likely influenced by sea water fluctuations. We analysed the community structure, specificity regarding seawater, and interindividual variability of 32–38 fish reared under ambient conditions. Additionally, we conducted an experiment to investigate the influence of acidification and a simplified heatwave on cod NM (three fish per replicate).This dataset is included in the OA-ICC data compilation maintained in the framework of the IAEA Ocean Acidification International Coordination Centre (see https://oa-icc.ipsl.fr). Original data were provided by the author of the related paper (see Related to) to the OA-ICC data curator. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2024) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2025-02-09.