In this study, we performed micro-scale dynamic laminar flow extraction and site-specific in situ chloride concentration measurements. Surface-enhanced Raman spectroscopy was utilized to investigate the diffusion process of chloride ions from an oil phase to a water phase under laminar flow. In contrast to common logic, we used SERS intensity gradients of Rhodamine 6G to quantitatively calculate the concentration of chloride ions at specific positions on a microfluidic chip. By varying the fluid flow rates, we achieved different extraction times and therefore different chloride concentrations at specific positions along the microchannel. SERS spectra from the water phase were recorded at these different positions, and the spatial distribution of the SERS signals was used to map the degree of nanoparticle aggregation. The concentration of chloride ions in the channel could therefore be obtained. We conclude that this method can be used to explore the extraction behaviour and efficiency of some ions or molecules that enhance the SERS intensity in water or oil by inducing nanoparticle aggregation.