The increased levels of organic carbon in sewage wastewater during recent years impose a great challenge to the existing wastewater treatment process (WWTP). Technological innovations are therefore sought that can reduce the release of organic carbon into lakes and seas. In the present study, magnetic nanoparticles (NPs) were synthesized, functionalized with poly(ethylenimine) (PEI), and characterized using TEM (transmission electron microscopy), X-ray diffraction (XRD), FTIR (Fourier transform infrared spectroscopy), CCS (confocal correlation spectroscopy), SICS (scattering interference correlation spectroscopy), magnetism studies, and thermogravimetric analysis (TGA). The removal of total organic carbon (TOC) and other contaminants using PEI-coated magnetic nanoparticles (PEI-NPs) was tested in wastewater obtained from the Hammarby Sjostadsverk sewage plant, Sweden. The synthesized NPs were about 12 nm in diameter and showed a homogeneous particle size distribution in dispersion by TEM and CCS analyses, respectively. The magnetization curve reveals superparamagnetic behavior, and the NPs do not reach saturation because of surface anisotropy effects. A 50% reduction in TOC was obtained in 60 min when using 20 mg/L PEI-NPs in 0.5 L of wastewater. Along with TOC, other contaminants such as turbidity (89%), color (86%), total nitrogen (24%), and microbial content (90%) were also removed without significant changes in the mineral ion composition of wastewater. We conclude that the application of PEI-NPs has the potential to reduce the processing time, complexity, sludge production, and use of additional chemicals in the WWTP.