Silica nanoparticles (SiNPs) are widely used in various fields, and they form nanofluids with exceptional properties when they are suspended in a base fluid. However, the transport and quantification of SiNPs in porous media pose significant challenges. To address this, fluorescence spectroscopy is a promising technique for this task. In this study, a series of core-shell silica-based fluorescent nanoparticles (FSiNPs) with similar cores but different surface groups were synthesized using the Stober and WORM synthesis methods. These hybrid FSiNPs were designed and presented the same colloidal behavior as commercial SiNPs widely applied in the form of nanofluids. The presence of primary amino groups was confirmed in positive-FSiNPs, and a posterior characterization supported the presence of organic matter in nanoparticles confirming the insertion of fluorescent molecules in all FSiNPs. Comparative analyses revealed that the WORM method produced more homogeneous nanoparticles with consistent form and size distribution. The N2 adsorption/desorption analysis demonstrated similarities between the synthesized FSiNPs and commercial SiNPs, validating their suitability for transport experiments focusing on colloidal behavior. Both WORM-FSiNPs were successfully quantified in the effluent after flowing through the glass bead column. The SiNP-containing aminopropyl surface groups showed the greatest stability and lowest adsorption compared with those grafted with silanol groups. It was attributed to the effect of stronger attractive interactions between the NPs and anionic surfactant molecules. The potential of these fluorescent NPs as sensitive tracers for transport and adsorption studies in nanofluids containing surfactants was demonstrated.