AbstractCarbon dioxide injection into deep saline aquifers is governed by a number of physico-chemical processes including mineral dissolution and precipitation, multiphase fluid flow, and capillary trapping. These processes can be coupled; however, the impact of fluid–rock reaction on the multiphase flow properties is difficult to study and is not simply correlated with variations in porosity. We observed the impact of rock mineral dissolution on multiphase flow properties in two carbonate rocks with distinct pore structures. Observations of steady-state $$\hbox {N}_2$$N2–water relative permeability and residual trapping were obtained, along with mercury injection capillary pressure characteristics. These tests alternated with eight stages in which 0.5% of the mineral volume was uniformly dissolved into solution from the rock cores using an aqueous solution with a temperature-controlled acid. Variations in the multiphase flow properties did not relate simply to changes in porosity, but corresponded to the changes in the underlying pore structure. In the Ketton carbonate, dissolution resulted in an increase in the fraction of pore volume made up by the smallest pores and a decrease in the fraction made up by the largest pores. This resulted in an increase in the relative permeability to the nonwetting phase, a decrease in the relative permeability to the wetting phase, and a modest, but systematic decrease in residual trapping. In the Estaillades carbonate, dissolution resulted in an increase in the fraction of pore volume made up by pores in the central range of the initial pore size distribution, and a corresponding decrease in the fraction made up by both the smallest and largest pores. This resulted in a decrease in the relative permeability to both the wetting and nonwetting fluid phases and no discernible impact on the residual trapping. In summary, the impact of rock matrix dissolution will be strongly dependent on the impact of that dissolution on the underlying pore structure of the rock. However, if the variation in pore structure can be observed or estimated with modelling, then it should be possible to estimate the impacts on multiphase flow properties.