Although the sorption of uranyl ions and other heavy metal ions over magnetic nanoparticles is well reported, the parameters governing the sorption process over the magnetic nanoparticles have not been clearly enumerated. However, to increase the efficiency of the sorption over the surface of these magnetic nanoparticles, it is essential to understand the different structural parameters that are involved in the sorption process. The sorption of uranyl ions and other competitive ions in simulated urine samples at different pH was effectively accomplished over magnetic nanoparticles of Fe₃O₄ (MNPs) and Mn-doped Fe₃O₄ (Mn-MNPs). The MNPs and Mn-MNPs were synthesized using an easily modified co-precipitation method and were thoroughly characterised using several techniques, such as XRD, HRTEM, SEM, zeta potential, and XPS. The substitutional doping of Mn (1 to 5 at%) in the Fe₃O₄ lattice (Mn-MNPs) showed better sorption ability as compared to that of MNPs. The sorption properties of these nanoparticles were mainly correlated with the different structural parameters to understand the roles of surface charge and different morphological parameters. The interaction centres over the surface of MNPs with the uranyl ions were designated and the effects of ionic interactions with uranyl ions for these sites were calculated. Extensive XPS, ab initio calculations and zeta potential studies have provided deep insights into the different aspects that play key roles in the sorption process. These materials showed one of the best K_d values (∼3 × 10⁶ cm³) in a neutral medium with very low t_1/2 values (∼0.9 min). The fast sorption kinetics (very low t_1/2) makes them amongst the best sorption materials for uranyl ions and optimal for the quantification of ultra-low-level uranyl ions in simulated bioassays.