Flow field-flow fractionation (FlFFF) with inductively coupled plasma mass spectrometric (ICP-MS) detection was applied for estimating the hydrodynamic diameter of gold nanoparticles (AuNPs). Hydrodynamic diameters of AuNPs of the same core diameter but with different surface coatings were different because the coating agents and their properties were different. The challenge of this work is due to the fact that AuNPs with various types of surface coatings exhibited different interactions in the FlFFF channel, leading to different retention behaviors. Therefore, we are interested in finding suitable FlFFF conditions for estimating the hydrodynamic diameter of AuNPs with various types of electrostatic stabilizing agents [tannic acid (TA) and citrate (CT)] and steric stabilizing agents [polyethylene glycol (PEG), polyvinylpyrrolidone (PVP), and branched polyethylene imine (BPEI)]. Different types of carrier liquids (DI water, 0.02% FL-70, 0.05% SDS, and 30 mM Tris buffer) and membrane materials [regenerated cellulose (RC) and polyethersulfone (PES) membranes] were investigated. Generally, FlFFF was applied for size characterization of nanoparticles based on FlFFF theory but the interactions between AuNPs and membrane affected the retention and the experimentally obtained hydrodynamic diameters of AuNPs from the FlFFF system. With DI water as a carrier liquid with RC or PES membranes, the hydrodynamic diameters of negatively charged particles (TA-, CT-, PVP-, and PEG-stabilized AuNPs) from FlFFF corresponded well with the hydrodynamic diameters from dynamic light scattering (DLS). Interestingly, it was possible to estimate hydrodynamic diameters of AuNPs in the mixture by using FlFFF whereas it was not possible with the use of DLS within the size range studied. This work summarized the possible interactions between AuNPs with various coating agents and membrane materials in different carrier liquids to give guidelines on the suitable conditions of FlFFF for further applications on AuNP hydrodynamic diameter estimation.