In complex large-scale systems such as climate, important effects are caused by a combination of confounding processes that are not fully observable. The identification of sources from observations of system state is vital for attribution and prediction, which inform critical policy decisions. The difficulty of these types of inverse problems lies in the inability to isolate sources and the cost of simulating computational models. Surrogate models may enable the many-query algorithms required for source identification, but data challenges arise from high dimensionality of the state and source, limited ensembles of costly model simulations to train a surrogate model, and few and potentially noisy state observations for inversion due to measurement limitations. The influence of auxiliary processes adds an additional layer of uncertainty that further confounds source identification. We introduce a framework based on (1) calibrating deep neural network surrogates to the flow maps provided by an ensemble of simulations obtained by varying sources, and (2) using these surrogates in a Bayesian framework to identify sources from observations via optimization. Focusing on an atmospheric dispersion exemplar, we find that the expressive and computationally efficient nature of the deep neural network operator surrogates in appropriately reduced dimension allows for source identification with uncertainty quantification using limited data. Introducing a variable wind field as an auxiliary process, we find that a Bayesian approximation error approach is essential for reliable source inversion when uncertainty due to wind stresses the algorithm.