An example implementation of a method for mapping tissue magnetic susceptibility includes acquiring magnetic resonance (MR) images acquired at multiple echo times, where the MR images correspond to a subject comprising at least two species of protons, and where each species has a different chemical shift in its respective resonance frequency. The method also includes determining, for each species, an estimated chemical shift value, determining an estimated map of magnetic field inhomogeneity based on the estimated chemical shift values, determining an estimated susceptibility distribution of the subject and an error of each estimated chemical shift value based on the estimated map of magnetic field inhomogeneity and prior information regarding the subject, and generating an image of the subject based on the estimated susceptibility distribution.
