The rising use of surface-modified engineered nanoparticles (ENPs) will result in their increased presence in aquatic environments; hence, a better understanding of their environmental fate is needed. In this study, silicon nanocrystals (Si-NCs) capped with organic acids of varying alkyl-chain length were used as model functionalized ENPs. Particle deposition kinetics were evaluated using sand-packed columns and a quartz crystal microbalance with dissipation monitoring (QCM-D). In general, an increase in solution ionic strength resulted in increased particle deposition in both columns and the QCM-D. However, the overall trends in Si-NC deposition with regard to alkyl-chain length differed in the two experimental systems, revealing how the system geometry can play a key role in defining the contribution of different particle retention mechanisms. To interpret these differences in the Si-NC deposition behavior, multiple characterization techniques were used: dynamic light scattering, nanoparticle tracking analysis, scanning ion occlusion sensing, and laser Doppler velocimetry. QCM-D also revealed insights into the influence of the particle surface coatings on particle stability. The ratio of the two QCM-D output parameters revealed that the rigidity of the particle-collector interfacial bonds varied with the alkyl-chain length, whereby particles capped with longer alkyl chains were less rigidly attached to the silica surface. Moreover, it is shown that the interpretation of ENP deposition behavior using QCM-D is limited by the presence of large-particle aggregates ( ‡ 700 nm in this study) which do not fully couple to the QCM-D sensor. Under such conditions, QCM-D measurements of ENP deposition should be interpreted with caution as the microbalance response cannot be directly considered as deposited mass. This study improves our understanding of the role that surface modifiers and ENP aggregates play in ENP deposition kinetics in efforts to predict the transport and fate of ENPs in natural and engineered aquatic environments.