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Abstract Injecting fluids into deep underground geologic structures is a critical component to development of long-term strategies for managing greenhouse gas emissions and facilitating energy extraction operations. Recently, we reported that metal–organic frameworks are low-frequency, absorptive-acoustic metamaterial that may be injected into the subsurface to enhance geophysical monitoring tools used to track fluids and map complex structures. A key requirement for this nanotechnology deployment is transportability through porous geologic media without being retained by mineral-fluid interfaces. We used flow-through column studies to estimate transport and retention properties of five different polymer-coated MIL-101(Cr) nanoparticles (NP) in siliceous porous media. When negatively charged polystyrene sulfonate coated nanoparticles (NP-PSS-70K) were transported in 1 M NaCl, only about 8.4% of nanoparticles were retained in the column. Nanoparticles coated with polyethylenimine (NP-PD1) exhibited significant retention (> 50%), emphasizing the importance of complex nanoparticle-fluid-rock interactions for successful use of nanofluid technologies in the subsurface. Nanoparticle transport experiments revealed that nanoparticle surface characteristics play a critical role in nanoparticle colloidal stability and as well the transport.