Water-fat separation is a non-linear non-convex parameter estimation problem in magnetic resonance imaging typically solved using spatial constraints. However, there is still limited knowledge on how to separate in vivo three chemical species in the presence of magnetic field inhomogeneities. The proposed method uses multiple graph-cuts in a hierarchical multi-resolution framework to perform robust chemical species separation in the breast for subjects with and without silicone implants. Experimental results show that the proposed method can decrease the computational time for water-fat separation and perform accurate water-fat-silicone separation with only a limited number of acquired echo images at 3 T. The silicone-separated images have an improved spatial resolution and image contrast compared to conventional scans used for regular monitoring of the silicone implant's integrity.