A method and apparatuses are provided to perform chemical species separation in magnetic resonance (MR) imaging (MRI). At least three MR images corresponding respectively to different echo times are obtained and represent signals from multiple chemical species including a first species and a second species in a tissue. A plurality of dual-echo pairs is selected from the at least three MR images. For each pair, a set of dual-echo separated images including a B0 field map, a first image for the first species, and a second image for the second species is estimated. An initial set of combined images including at least one of: an initial combined B0 field map, first, and second image is generated by combining at least one of: two or more of the B0 field maps, two or more of the first images, and two or more of the second images.