The estimation of unknown values of parameters (or hidden variables, control variables) that characterise a physical system often relies on the comparison of measured data with synthetic data produced by some numerical simulator of the system as the parameter values are varied. This process often encounters two major difficulties: the generation of synthetic data for each considered set of parameter values can be computationally expensive if the system model is complicated; and the exploration of the parameter space can be inefficient and/or incomplete, a typical example being when the exploration becomes trapped in a local optimum of the objection function that characterises the mismatch between the measured and synthetic data. A method to address both these issues is presented, whereby: a surrogate model (or proxy), which emulates the computationally expensive system simulator, is constructed using deep recurrent networks (DRN); and a nested sampling (NS) algorithm is employed to perform efficient and robust exploration of the parameter space. The analysis is performed in a Bayesian context, in which the samples characterise the full joint posterior distribution of the parameters, from which parameter estimates and uncertainties are easily derived. The proposed approach is compared with conventional methods in some numerical examples, for which the results demonstrate that one can accelerate the parameter estimation process by at least an order of magnitude.