A computer implemented stochastic inversion method for estimating model parameters of an earth model. In an embodiment, the method utilizes a sampling-based stochastic technique to determine the probability density functions (PDF) of the model parameters that define a boundary-based multi-dimensional model of the subsurface. In some embodiments a sampling technique known as Markov Chain Monte Carlo (MCMC) is utilized. MCMC techniques fall into the class of “importance sampling” techniques, in which the posterior probability distribution is sampled in proportion to the model's ability to fit or match the specified acquisition geometry. In another embodiment, the inversion includes the joint inversion of multiple geophysical data sets. Embodiments of the invention also relate to a computer system configured to perform a method for estimating model parameters for accurate interpretation of the earth's subsurface.