In situ magnetic capturing and surface-enhanced Raman scattering (SERS) detection techniques can be used for detecting microbial contamination and uremic toxins. Magnetic SERS substrates were fabricated using immobilized gold nanoparticles (AuNPs) and iron-oxide (Fe3O4) nanoparticles on exfoliated nanoscale silicate platelets (NSPs). The prepared magnetic SERS nanosheets (Fe3O4@AuNPs@NSP nanosheets) were able to not only magnetically capture bacteria and biomolecules but also effectively induce the hot-spot effect and enhance the Raman signal by the surface plasmon resonance of the AuNP arrays. The results showed that both the ratio of AuNPs to Fe3O4 nanoparticles and the order of immobilization on the NSP nanosheets are important factors for inducing magnetic capturing behavior and SERS sensitivity. A method that yielded magnetic capturing behavior was to graft AuNPs on NSP nanosheets first, followed by the immobilization of Fe3O4 nanoparticles. Fe3O4@AuNPs@NSP nanosheets prepared using 0.9 mM HAuCl4 displayed the highest magnetic capturing behavior and SERS enhancement effect, showing an optimal interparticle gap. The bacteria (Escherichia coli) were captured and separated by the magnetic SERS substrates using an applied magnetic field, and then the magnetically captured samples were monitored by Raman spectroscopy for rapid SERS detection. Furthermore, the SERS sensitivity increased by ~2 times after magnetic capturing, and the limit of detection for sensing bacteria was below 103 CFU/mL. The novel magnetic SERS substrates provide ultrasensitive, rapid, and reproducible SERS detection for magnetically capturing biomolecules (bacteria, uremic toxins, and parathyroid hormone) and can be applied in environmental, water, and biomedical detection.