Engineered nanoporous particles have become an important class of nanostructured materials that have been increasingly applied in energy, biomedical, and environmental researches and industries. The internal pore surfaces in the particles can be chemically functionalized for environmental applications to sequestrate metals and radionuclide contaminants from groundwater. The fate and transport of the nanoporous particles in subsurface environments, however, have not been studied. Here we present a scanning optical fiber fluorescence profiler that can be used to in situ monitor the transport of fluorescent particles in column systems. Engineered nanoporous silicate particles (ENSPs) that were covalently bounded with fluorescence-emitting, and uranium-chelating ligands in the intraparticle pore domains were synthesized and used as an example to investigate nanoporous particle transport and to demonstrate the application of the developed in situ measurement profiler. The profiler detected an “irreversible” or slowly detached fraction of ENSPs in a sand collector even under thermodynamically unfavorable conditions for particle attachment. Further, the in situ measurement system detected the spatial variability of ENSPs transport that deviated from one-dimensional, homogeneous assumption, which is typically used to model particle transport in column systems. Generally, however, both measured and model-calculated results indicated that the transport of ENSPs was consistent with that of nonporous colloidal particles subjected to coupled reversible attachment/detachment and straining processes. The developed system can also be applied to detect other fluorescent nanostructured or colloidal particles in porous media.