Numerical modeling is an essential tool for geoscience applications involving multiphase flow behavior. Performing numerical simulation is, however, computationally intensive due to multi-scale, non-linear, and multi-physics nature of mechanisms controlling multiphase flow dynamics. Additionally, the computational challenges associated with traditional numerical simulations limit their applicability for repetitive simulations required in inverse modeling, uncertainty analysis, and optimization tasks. To overcome these limitations, surrogate modeling has recently emerged as a viable solution. A surrogate model, which functions as a regression model, is trained using numerical simulation data. It approximates the input–output relationships within a dynamic fluid environment. We design surrogate models, based on conditional deep convolutional generative adversarial network (cDC-GAN), to map the cross-domain between input and output pairs in a multiphase multicomponent system, focusing on methane (CH4) migration in shallow unconfined aquifers. The cDC-GAN technique is selected due to its ability to generate high-fidelity surrogate models that effectively capture complex spatial distributions and heterogeneities. This technique excels in handling high-dimensional data, learning the intricate relationships between inputs and outputs, and producing realistic representations of subsurface phenomena. The trained cDC-GANs consider capillary entry pressure heterogeneity as input because this geologic attribute places first-order control on CH4 migration in subsurface. The outputs include CH4 saturation, water saturation, residual saturation of CH4, CH4 mole fraction, and CH4 molality. For each output, a separate cDC-GAN model is trained. Once trained, cDC-GANs can at any given time determine CH4 distribution in a shallow unconfined aquifer, both qualitatively and quantitatively. The cDC-GAN approach can be considered as a valuable complement to numerical simulations for predicting multiphase flow behavior in other geoscience-, energy-, and environmental applications such as contaminant transport, hydrocarbon production, and geological carbon dioxide and hydrogen storage.