Sol-gel technology is a versatile tool for preparation of complex silica-based materials with targeting functions for use as adsorbents in water purification. Most efficient removal of organic pollutants is achieved by using enzymatic reagents grafted on nano-carriers. However, enzymes are easily deactivated in the presence of heavy metal cations. In this work, we avoided inactivation of immobilized urease by Cu (II) and Cd (II) ions using magnetic nanoparticles provided with additional complexonate (diethylene triamine pentaacetic acid or DTPA) functions. Obtained nanomaterials were characterized by Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and scanning electron microscopy (SEM). According to TGA, the obtained Fe3O4/SiO2-NH2-DTPA nanoadsorbents contained up to 0.401 mmol/g of DTPA groups. In the concentration range Ceq = 0–50 mmol/L, maximum adsorption capacities towards Cu (II) and Cd (II) ions were 1.1 mmol/g and 1.7 mmol/g, respectively. Langmuir adsorption model fits experimental data in concentration range Ceq = 0–10 mmol/L. The adsorption mechanisms have been evaluated for both of cations. Crosslinking of 5 wt % of immobilized urease with glutaraldehyde prevented the loss of the enzyme in repeated use of the adsorbent and improved the stability of the enzymatic function leading to unchanged activity in at least 18 cycles. Crosslinking of 10 wt % urease on the surface of the particles allowed a decrease in urea concentration in 20 mmol/L model solutions to 2 mmol/L in up to 10 consequent decomposition cycles. Due to the presence of DTPA groups, Cu2+ ions in concentration 1 µmol/L did not significantly affect the urease activity. Obtained magnetic Fe3O4/SiO2-NH2-DTPA-Urease nanocomposite sorbents revealed a high potential for urease decomposition, even in presence of heavy metal ions.