The water uptake behavior of atmospheric aerosol dictates their climate effects. In many studies, aerosol particles are deposited onto solid substrates to measure water uptake; however, the effects of the substrate are not well understood. Furthermore, in some cases, methods used to analyze and quantify water uptake of substrate deposited particles use a two-dimensional (2D) analysis to monitor growth by following changes in the particle diameter with relative humidity (RH). However, this 2D analysis assumes that the droplet grows equally in all directions. If particle growth is not isotropic in height and diameter, this assumption can cause inaccuracies when quantifying hygroscopic growth factors (GFs), where GF for a for a spherical particle is defined as the ratio of the particle diameter at a particular relative humidity divided by the dry particle diameter (typically about 5% RH). However, as shown here, anisotropic growth can occur in some cases. In these cases, a three-dimensional (3D) analysis of the growth is needed. This study introduces a way to quantify the hygroscopic growth of substrate deposited particles composed of model systems relevant to atmospheric aerosols using atomic force microscopy (AFM), which gives information on both the particle height and area and thus a three-dimensional view of each particle. In this study, we compare GFs of submicrometer sized particles composed of single component sodium chloride (NaCl) and malonic acid (MA), as well as binary mixtures of NaCl and MA, and NaCl and nonanoic acid (NA) determined by AFM using area (2D) equivalent diameters, similar to conventional microscopy methods, to GFs determined using volume (3D) equivalent diameter. We also compare these values to GFs determined by a hygroscopic tandem differential mobility analyzer (HTDMA; substrate free, 3D method). It was found that utilizing volume equivalent diameter for quantifying GFs with AFM agreed well with those determined by substrate-free HTDMA method, regardless of particle composition but area equivalent derived GFs varied for different chemical systems. Furthermore, the NaCl and MA mixture was substrate-deposited both wet and dry, revealing that the hydration state of the particle at the time of impaction influences how the particle grows on the substrate upon water uptake. Most importantly, for the binary mixtures it is shown here that different populations of particles can be distinguished with AFM, an individual particle method, whereas HTDMA sees the ensemble average. Overall, this study establishes the methodology of using AFM to accurately quantify the water uptake of individual submicrometer particles at ambient conditions over a wide range of RH values. Furthermore, the importance of single particle AFM analysis is demonstrated.