Abstract: Source term estimation (STE) of hazardous material (HAZMAT) releases is critical for emergency response. Such problem is usually solved with the aid of atmospheric dispersion modelling and inversion algorithms accompanied with a variety of uncertainty, including uncertainty in atmospheric dispersion models, uncertainty in meteorological data, uncertainty in measurement process and uncertainty in inversion algorithms. Bayesian inference methods provide a unified framework for solving STE problem and quantifying the uncertainty at the same time. In this paper, three stochastic methods for STE, namely Markov chain Monte Carlo (MCMC), sequential Monte Carlo (SMC) and ensemble Kalman filter (EnKF), are compared in accuracy, time consumption as well as the quantification of uncertainty, based on which a kind of flip ambiguity phenomenon caused by various uncertainty in STE problems is pointed out. The advantage of non-Gaussian estimation methods like SMC is emphasized.