In recent years, water pollution and pesticide accumulation in the food chain have become a serious environmental and health hazard problem. Direct determination of these contaminants is a difficult task due to their low concentration level and the matrix interferences. Therefore, an efficient separation and preconcentration procedure is often required prior to the analysis. With the advancement in nanotechnology, various types of magnetic core–shell nanoparticles have successfully been synthesized and received considerable attention as sorbents for decontamination of diverse matrices. Magnetic core–shell nanoparticles with surface modifications have the advantages of large surface-area-to-volume ratio, high number of surface active sites, no secondary pollutant, and high magnetic properties. Due to their physicochemical properties, surface-modified magnetic core–shell nanoparticles exhibit high adsorption efficiency, high rate of removal of contaminants, and easy as well as rapid separation of adsorbent from solution via external magnetic field. Such facile separation is essential to improve the operation efficiency. In addition, reuse of nanoparticles would substantially reduce the treatment cost. In this review article, we have attempted to summarize recent studies that address the preconcentration methods of pesticide residue analysis and removal of toxic contaminants from aquatic systems using magnetic core–shell nanoparticles as adsorbents.