► Application of soil gas and aquifers surveys in an natural gas storage site. ► Aquifers and soils are affected by shallow-derived degassing without any deep input. ► Gathered results represent the baseline for future storage purposes. A geochemical survey, in shallow aquifers and soils, has been carried out to evaluate the feasibility of natural gas (CH4) storage in a deep saline aquifer at Rivara (MO), Northern Italy. This paper discusses the areal distribution of CO2 and CH4 fluxes and CO2, CH4, Rn, He, H2 concentrations both in soils and shallow aquifers above the proposed storage reservoir. The distribution of pathfinder elements such as 222Rn, He and H2 has been studied in order to identify potential faults and/or fractures related to preferential migration pathways and the possible interactions between the reservoir and surface. A geochemical and isotopic characterization of the ground waters circulating in the first 200m has allowed to investigation of (i) the origin of the circulating fluids, (ii) the gas–water–rock interaction processes, (iii) the amount of dissolved gases and/or their saturation status. In the first 200m, the presence of CH4-rich reducing waters are probably related to organic matter (peat) bearing strata which generate shallow-derived CH4, as elsewhere in the Po Plain. On the basis of isotopic analysis, no hints of thermogenic CH4 gas leakage from a deeper reservoir have been shown. The δ13C(CO2) both in ground waters and free gases suggests a prevalent shallow origin of CO2 (i.e. organic and/or soil-derived). The acquisition of pre-injection data is strategic for the natural gas storage development project and as a baseline for future monitoring during the gas injection/withdrawing period. Such a geochemical approach is considered as a methodological reference model for future CO2/CH4 storage projects.