Magnetic nanoparticles (MNPs) were modified by hyaluronic acid (HA). After the process of functionalization, two different strategies have been used to immobilize isocitrate dehydrogenases (IDH) on MNPs. In the first strategy, cross-linked enzyme aggregates were prepared. For this, firstly hyaluronic acid modified magnetic nanoparticles cross-linked enzyme fine aggregates of isocitrate dehydrogenases (IDH/HA/MNPs-CLEAs) were synthesized, and secondly bovine serum albumin (BSA) as co-feeder was used to synthesize the IDH/BSA/HA/MNPs-CLEAs. In the second strategy, the IDH was effectively immobilized on the HA/MNPs surface. The features of MNPs and its derivatives have been studied by X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier transforms infrared spectroscopy (FTIR), vibrating sample magnetometer (VSM), and zeta potential measurements. The activity and stability of IDH in IDH/HA/MNPs, IDH/HA/MNPs-CLEAs, and IDH/BSA/HA/MNPs-CLEAs were enhanced. Besides, the enzyme immobilized was readily separated via external magnet from the reaction medium and reused many times. The acquired findings indicate that HA/MNPs are a novel binder/support system to IDH, and IDH immobilized on this system can become a very important biocatalyst working with high accuracy and sensitivity for the determination of magnesium in drinking water and other biological solutions.