A water- and fat-suppressed sequence is typically used to verify the integrity of silicone breast implants. The feasibility of using chemical shift encoding-based MRI for in vivo water–fat–silicone separation was recently shown. In this work, a hierarchical multi-resolution graph-cut framework is developed and proposed for water–fat–silicone separation in breast MRI. Robustness and competitive processing times are achieved by performing graph-cuts using varying spatial resolution. Results show successful water–fat–silicone separation for 4 echoes (the minimum of required echoes) without water–fat–silicone swaps and an improved silicone contrast compared to the conventional sequence.