Subsurface remediation often involves reconstruction of contaminant release history from sparse observations of solute concentration. Markov Chain Monte Carlo (MCMC), the most accurate and general method for this task, is rarely used in practice because of its high computational cost associated with multiple solves of contaminant transport equations. We propose an adaptive MCMC method, in which a transport model is replaced with a fast and accurate surrogate model in the form of a deep convolutional neural network (CNN). The CNN-based surrogate is trained on a small number of the transport model runs based on the prior knowledge of the unknown release history. Thus reduced computational cost allows one to reduce the sampling error associated with construction of the approximate likelihood function. As all MCMC strategies for source identification, our method has an added advantage of quantifying predictive uncertainty and accounting for measurement errors. Our numerical experiments demonstrate the accuracy comparable to that of MCMC with the forward transport model, which is obtained at a fraction of the computational cost of the latter.