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Super paramagnetic iron oxide nanoparticles (SPIONs) (∼12 nm) were synthesized as the magnetic core for an imprinted polymer (MIP) shell using 4-vinylpyridine as the functional monomer and trimethylolpropane trimethacrylate (TRIM) as the cross-linker, bringing the average size up to ∼45 nm. Five targets were imprinted—the Selective Androgen Receptor Modulators (SARMs) andarine, ligandrol and RAD-140; and the steroids estradiol and gestrinone. All MMIPs produced good selectivity when loaded with a non-target molecule, with all calculated selectivity factors above the 1.2 recommended threshold and also demonstrated good affinity/capacity. The rebinding of the target molecules from a complex matrix was also explored by using spiked river water samples. The SARMs-based MMIPs were able to rebind 99.56, 87.63 and 72.78% of their target molecules (andarine, ligandrol and RAD-140, respectively), while the steroidal-based MMIPs were able to rebind 64.54 and 55.53% of their target molecules (estradiol and gestrinone, respectively) at a nominal loading of 20 ≈ μ g in 50 mg of NPs. This work highlights the potential of these bi-functional materials for trace material clean-up of complex samples and/or subsequent analysis and opens up possibilities for further simple, rapid-to-synthesise materials for targeted clean-up.