A clear understanding of the factors controlling the deposition behavior of engineered nanoparticles (ENPs), such as quantum dots (QDs), is necessary for predicting their transport and fate in natural subsurface environments and in water filtration processes. A quartz crystal microbalance with dissipation monitoring (QCM-D) was used to study the effect of particle surface coatings and water chemistry on the deposition of commercial QDs onto Al2O3. Two carboxylated QDs (CdSe and CdTe) with different surface coatings were compared with two model nanoparticles: sulfate-functionalized (sPL) and carboxyl-modified (cPL) polystyrene latex. Deposition rates were assessed over a range of ionic strengths (IS) in simple electrolyte (KCl) and in electrolyte supplemented with two organic molecules found in natural waters; namely, humic acid and rhamnolipid. The Al2O3 collector used here is selected to be representative of oxide patches found on the surface of aquifer or filter grains. Deposition studies showed that ENP deposition rates on bare Al2O3 generally decreased with increasing salt concentration, with the exception of the polyacrylic-acid (PAA) coated CdTe QD which exhibited unique deposition behavior due to changes in the conformation of the PAA coating. QD deposition rates on bare Al2O3 were approximately 1 order of magnitude lower than those of the polystyrene latex nanoparticles, likely as a result of steric stabilization imparted by the QD surface coatings. Adsorption of humic acid or rhamnolipid on the Al2O3 surface resulted in charge reversal of the collector and subsequent reduction in the deposition rates of all ENPs. Moreover, the ratio of the two QCM-D output parameters, frequency and dissipation, revealed key structural information of the ENP-collector interface; namely, on bare Al2O3, the latex particles were rigidly attached as compared to the more loosely attached QDs. This study emphasizes the importance of considering the nature of ENP coatings as well as organic molecule adsorption onto particle and collector surfaces to avoid underestimating ENP mobility in natural and engineered aquatic environments.