The synthesis and the characterization of three kinds of labeled silica nanoparticles were performed. Three different labeling strategies were investigated: fluorescent organic molecule (FITC) embedded in silica matrix, heavy metal core (Ag(0)) and radioactive core ((110m)Ag) surrounded by a silica shell. The main properties and the suitability of each kind of labeled nanoparticle in terms of size, surface properties, stability, detection limits, and cost were determined and compared regarding its use for transport studies. Fluorescent labeling was found the most convenient and the cheapest, but the best detection limits were reached with chemical (Ag(0)) and radio-labeled ((110m)Ag) nanoparticles, which also allowed nondestructive quantifications. This work showed that the choice of labeled nanoparticles as surrogates of natural colloids or manufactured nanoparticles strongly depends on the experimental conditions, especially the concentration and amount required, the composition of the effluent, and the timescale of the experiment.