We synthesize a high-efficiency substrate for surface-enhanced Raman scattering (SERS) measurements, which is composed of gold nanoparticles (AuNPs) on two-dimensional silicate nanoplatelets acting as an inorganic stabilizer, via the in-situ reduction of hydrogen tetrachloroaurate (III) by sodium citrate in an aqueous solution. Silicate platelets of ~1-nm thickness and various sizes, viz. laponite (50 nm), sodium montmorillonite (Na+–MMT, 100 nm), and mica (500 nm), are used to stabilize the AuNPs (Au@silicate), which are formed with uniform diameters ranging between 25 and 30 nm as confirmed by transmission electron microscopy (TEM). In particular, the laponite SERS substrate can be used in biological, environmental, and food safety applications to measure small molecules such as DNA (adenine molecule), dye (Direct Blue), and herbicide (paraquat) as it shows high detection sensitivity with a detection limit of 10−9 M for adenine detection. These highly sensitive SERS substrates, with their three-dimensional hot-junctions formed with AuNPs and two-dimensional silicate nanoplatelets, allow the highly efficient detection of organic molecules. Therefore, these Au@silicate nanohybrid substrates have great potential in biosensor technology because of their environmentally-friendly and simple fabrication process, high efficiency, and the possibility of rapid detection.