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Carbonate Stimulation is a practical approach to increase well productivity. The use of reactive fluids in the treatment helps open a conductive path (wormhole) for hydrocarbon flow. Reactive transport modeling is used to understand this process and optimize the treatment. This process occurs at different length scales such as Darcy’s and pore scale. Thus, the parameters used in the simulation model are subjected to uncertainty, which affects the model’s predictability and stimulation optimization. In this work, we adopted an integrated uncertainty framework that combines a two-scale continuum model, design of experiments (DoE), and Sobol sensitivity method. This approach helps study wormhole propagation in carbonate rocks during acidizing treatment and investigate the impact of input parameters uncertainty on the selected model response such as pore volume to breakthrough and the increase in the effective permeability.