Hydrophobic silver (Ag) nanoparticles of ∼16 nm diameter were self-assembled as building blocks in an emulsion to form large spherical clusters upon the removal of organic solvents. The self-assembled clusters of Ag nanoparticles have diameters in the range 0.5–1.0 μm and are composed of thousands of densely packed Ag nanoparticles, leading to the generation of multiple active sites or hot spots for surface-enhanced Raman scattering (SERS) in a single cluster, as clearly observed using confocal Raman microscopy. Such single clusters of Ag nanoparticles show significant SERS activity for Rhodamine-6G and dithiocarbamates such as thiram. The enhancement factor for R6G was calculated to reach 1 × 10⁹, which is possible for the observation of SERS signals of a single molecule of R6G according to literature reports. The as-prepared individual clusters of Ag nanoparticles have been demonstrated for the SERS detection of the agricultural chemical thiram. The results show that the detection limit for thiram is as low as 0.024 ppm, which is much lower than the maximal residue limit (MRL) of 7 ppm in fruit prescribed by U.S. Environmental Protection Agency (EPA). The system also possesses the ability to selectively detect dithiocarbamate compounds over other types of agricultural chemical. Furthermore, spiked and recovery tests show that the Ag nanoparticle clusters can be used to detect thiram in natural lake water and commercial apple juice without much interference.