The design, preparation process, binding abilities, morphological characteristic and prospective field of application of dummy-template magnetic molecularly imprinted polymer (DMMIP) for preliminary recognition of the selected low-mass polybrominated diphenyl ethers (PBDE-47 and PBDE-99) from aquatic environment were investigated. The surface of iron oxide (Fe3O4) nanopowder (50–100 nm particles size) was modified with tetraethoxysilane and next prepared Fe3O4@SiO2 particles were dispersed in anhydrous toluene functionalized by (3-aminopropyl)triethoxysilane. Finally, MIPs' thin film layer on the surface of Fe3O4@SiO2@NH2 was formed in acetonitrile as a solvent solution, using ethylene glycol dimethacrylate as the cross-linker, building monomer, 1,1′-Azobis(cyclohexanecarbonitrile) as the radical initiator, methacrylic acid as a functional monomer and 4,4′-Dihydroxydiphenyl ether as the dummy template molecule as a structural analogue of low-mass PBDEs. To characterize the chemical structure of prepared DMMIPs, the Fourier transform infrared spectroscopy analysis was performed. The specific surface area of the developed sorbent was estimated using Brauner-Emmet-Teller nitrogen adsorption/desorption analysis. To assess the average pore sizes, pore diameters and pore volumes of the prepared sorbent, the Barret-Joyner-Halenda technique was applied. The average values of imprinting factor for PBDE-47 and PBDE-99 were 11.3 ± 1.6 and 13.7 ± 1.2, respectively. The average value of recovery of PBDE-47 and PBDE-99 for developed DMMIPs from modelling water: methanol solution were 85.4 ± 6.7% and 86.4 ± 9.4%, respectively. In a case of spiked distilled water, tap water as well as local river water the calculated recovery values ranged from 65%% up to 82% and from 33% up to 76% for PBDE-47 and PBDE-99, respectively. Following the preliminary research on selected water samples, the proposed combination of imprinting technology and core–shell materials with magnetic properties might be considered as a promising sorption tool used for targeted recognition of low-mass PBDEs in aquatic solutions. Display omitted •The preparation process of core-shell magnetic DMIP for low-mass PBDEs was described.•The 4,4-Dihydroxydiphenyl ether was used as a dummy-template of low-mass PBDEs for magnetic MIP.•The morphological structure and binding abilities of prepared magnetic DMIP were investigated.•Synthesised magnetic DMIP shows sufficient specific recognition to low-mass PBDEs.•The application potential of prepared magnetic DMIP for targeted analytes in water samples was studied.