Display omitted •The shell in PHSNs resulted in significantly different particle physicochemical properties compared to SSNs of similar size.•Higher surface roughness in PHSNs than in SSNs was responsible for the reduced transport and deviations from DLVO theory.•High IS and low pH decreased mobility and increased retention for both particle populations.•Retention was 3-fold higher for PHSNs compared to SSNs at the highest IS and lowest pH. Silica nanoparticles (SiO2 NPs) are of increasing interest in nano-enabled agriculture, particularly as nanocarriers for the targeted delivery of agrochemicals. Their direct application in agricultural soils may lead to the release of SiO2 NPs in the environment. Although some studies have investigated transport of solid SiO2 NPs in porous media, there is a knowledge gap on how different SiO2 NP structures incorporating significant porosities can affect the mobility of such particles under different conditions. Herein, we investigated the effect of pH and ionic strength (IS) on the transport of two distinct structures of SiO2 NPs, namely solid SiO2 NPs (SSNs) and porous hollow SiO2 NPs (PHSNs), of comparable sizes (~200 nm). Decreasing pH and increasing ionic strength reduced the mobility of PHSNs in sand-packed columns more significantly than for SSNs. The deposition of PHSNs was approximately 3 times greater than that of SSNs at pH 4.5 and IS 100 mM. The results are non-intuitive given that PHSNs have a lower density and the same chemical composition of SSNs but can be explained by the greater surface roughness and ten-fold greater specific surface area of PHSNs, and their impacts on van der Waals and electrostatic interaction energies.