Our study is keyed to the development of a viable framework for the stochastic characterization of coreflooding simulation models under two- and three-phase flow conditions taking place within a core sample in the presence of preferential flow of the kind that can be associated with the presence of a system of fractures. We do so considering various modeling strategies based on (spatially homogeneous or heterogeneous) single- and dual-continuum formulations of black-oil computational models and relying on a global sensitivity-driven stochastic parameter calibration. The latter is constrained through a set of data collected under a water alternating gas scenario implemented in laboratory-scale coreflooding experiments. We set up a collection of Monte Carlo (MC) numerical simulations while considering uncertainty encompassing (a) rock attributes (i.e., porosity and absolute permeability), as well as (b) fluid–fluid/ fluid–solid interactions, as reflected through characteristic parameters of relative permeability and capillary pressure formulations. Modern moment-based global sensitivity indices are evaluated on the basis of the MC model responses, with the aim of (i) quantifying sensitivity of the coreflooding simulation results to variations of the input uncertain model parameters and (ii) assessing the possibility of reducing the dimensionality of model parameter spaces. We then rest on a stochastic inverse modeling approach grounded on the acceptance–rejection sampling (ARS) algorithm to obtain probability distributions of the key model parameters (as identified through our global sensitivity analyses) conditional to the available experimental observations. The relative skill of the various candidate models to represent the system behavior is quantified upon relying on the deviance information criterion. Our findings reveal that amongst all tested models, a dual-continuum formulation provides the best performance considering the experimental observations available. Only a few of the parameters embedded in the dual-continuum formulation are identified as major elements significantly affecting the prediction (and associated uncertainty) of model outputs, petrophysical attributes and relative permeability model parameters having a stronger effect than parameters related to capillary pressure.