The slow flocculation of silver nanoparticle (NP) aggregates obtained through p-mercaptobenzoic acid (MBA) linker molecules was analyzed by surface-enhanced Raman scattering (SERS) correlation spectroscopy. We demonstrate that our experimental setup, together with the quantitative exploitation of the SERS intensity autocorrelation functions (ACFs) measured from the MBA molecules, enables to determine quantitatively and in situ the size of the SERS active clusters. Moreover, we show that it is possible to characterize the different states of aggregation during cluster formation simply by measuring the size of such silver aggregates. This has been accurately performed for both larger-size aggregates down to very few NPs only. We finally show that our approach is also sensitive to detect and analyze the SERS signal obtained from MBA molecules sitting on nonaggregated NPs. These experiments pave the way to the in situ characterization of functionalized metal NPs as well as the in situ monitoring of NP aggregation, in conjunction with deriving the optical properties of the as-formed clusters.