We introduce a new methodology for inference of fluid composition from measurements of mineralogical or chemical compositions, expanding upon the use of reactive transport models to understand hydrothermal alteration processes. The reactive transport models are used to impute a latent variable explanatory mechanism in the formation of hydrothermal alteration zones and mineral deposits. An expectation maximisation algorithm is then employed to solve the joint problem of identifying alteration zones in the measured data and estimating the fluid composition, based on the fit between the mineral abundances in the measured and predicted alteration zones. Using the hydrothermal alteration of granite as a test case (greisenisation), a range of synthetic tests is presented to illustrate how the methodology enables objective inference of the mineralising fluid. For field data from the East Kemptville tin deposit in Nova Scotia, the technique generates inferences for the fluid composition which compare favourably with previous independent estimates, demonstrating the feasibility of the proposed calibration methodology.