Silica nanoparticles (SiNPs) have been extensively studied as additives in injected fluids for enhanced oil recovery. Typically, surfactants are used to increase colloidal stability, but little is known about the transport of SiNPs in porous media because of the scarcity of reliable quantification techniques. In this study, we investigated the use of core-shell silica-based fluorescent SiNPs as tracers for transport studies of nanofluids containing surfactants. Two synthetic strategies were used to obtain distinct structures of fluorescent SiNPs with similar cores but different surface groups, namely silanol and aminopropyl, comparable to those reported in nanofluid applications. The synthesised NPs had comparable sizes and morphologies but displayed opposite surface charges when dispersed in aqueous solutions. The main colloidal properties and time stability of the fluorescence response were determined in the presence of an anionic surfactant and compared with regard to their potential use as tracers for transport studies. Both fluorescent SiNPs 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. We attribute this behaviour to the effect of stronger attractive interactions between the NPs and surfactants. The potential of these fluorescent NPs as sensitive tracers for transport and adsorption studies in nanofluids containing surfactants was demonstrated.