A method and system comprising measuring concentrations of first and second isotopologues of a gas of interest within a first cavity that is sealably in contact with a soil location through an inlet membrane, and the first cavity being defined by chamber walls having openings covered by outlet membranes. Reference concentrations of the first and second isotopologues are measured in a second cavity having a closed bottom, the second cavity being defined by chamber walls having openings covered by more outlet membranes. Relative flux of the isotopologues can be calculated using the measured concentrations.