In Resin Transfer Moulding (RTM), local variations in reinforcement properties (porosity and permeability) and the formation of gaps along the reinforcement edges result in non-uniform resin flow patterns, which may cause defects in the produced composite component. The ensemble Kalman inversion (EKI) algorithm has previously been used to invert in-process data to estimate local reinforcement properties. However, implementation of this algorithm in some applications is limited by the requirement to run thousands of computationally expensive resin flow simulations. In this study, a machine learning approach is used to train a surrogate model which can emulate resin flow simulations near-instantaneously. A partition of the flow domain into a low-dimensional representation enables an artificial neural network (ANN) surrogate to make accurate predictions, with a simple architecture. When the ANN is integrated within the EKI algorithm, estimates for local reinforcement permeability and porosity can be achieved in real time, as was verified by virtual and lab experiments. Since EKI utilises the Bayesian framework, estimates are given within confidence intervals and statements can be made on-line regarding the probability of defects within sections of the reinforcement. The proposed framework has shown good predictive capabilities for the set of laboratory experiments and estimates for reinforcement properties were always computed within 1 s.