In the present study, we conducted mesocosm experiments to determine the shedding and decay rate constants of eDNA and eRNA in M. gigas (Magallana [Crassostrea] gigas) using mitochondrially encoded tRNA leucine 1 (mt-tl1) marker at various partial pressures of CO2 in seawater. To our knowledge, this is the first study manipulating seawater pH using CO2. We developed a sensitive and specific quantitative PCR-based assay to detect M. gigas eDNA and eRNA.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 2025-10-23.