The marine controlled-source electromagnetic (CSEM) technique is an application of electromagnetic (EM) waves to image the electrical resistivity of the subsurface underneath the seabed. The modeling of marine CSEM is a crucial and time-consuming task due to the complexity of its mathematical equations. Hence, high computational cost is incurred to solve the linear systems, especially for high-dimensional models. Addressing these problems, we propose Gaussian process (GP) calibrated with computer experiment outputs to estimate multi-frequency marine CSEM profiles at various hydrocarbon depths. This methodology utilizes prior information to provide beneficial EM profiles with uncertainty quantification in terms of variance (95% confidence interval). In this paper, prior marine CSEM information was generated through Computer Simulation Technology (CST) software at various observed hydrocarbon depths (250−2750 m with an increment of 250 m each) and different transmission frequencies (0.125, 0.25, and 0.5 Hz). A two-dimensional (2D) forward GP model was developed for every frequency by utilizing the marine CSEM information. From the results, the uncertainty measurement showed that the estimates were close to the mean. For model validation, the calculated root mean square error (RMSE) and coefficient of variation (CV) proved in good agreement between the computer output and the estimated EM profile at unobserved hydrocarbon depths.