Cetyltrimethylammonium bromide (CTAB) is a widely used surfactant that aids the aqueous synthesis of colloidal nanoparticles. However, the presence of residual CTAB on nanoparticle surfaces can significantly impact nanoparticle applications, such as catalysis and sensing, under hydrated conditions. As such, consideration of the presence and quantity of CTAB on nanoparticle surfaces under hydrated conditions is of significance. Herein, as part of an integrated material characterization framework, we demonstrate the feasibility of in situ atomic force microscopy (AFM) to detect CTAB on the surface of Au nanocubes (Au NCs) under hydrated conditions, which enabled superior characterization compared to conventional spectroscopic methods. In situ force-distance (FD) spectroscopy and Kelvin probe force microscopy (KPFM) measurements support additional characterization of adsorbed CTAB, while correlative in situ AFM and scanning electron microscopy (SEM) measurements were used to evaluate sequential steps of CTAB removal from Au NCs across hydrated and dehydrated environments, respectively. Notably, a substantial quantity of CTAB remained on the Au NC surface after methanol washing, which was detected in AFM measurements but was not detected in infrared spectroscopy measurements. Subsequent electrochemical cleaning was found to be critically important to remove CTAB from the Au NC surface. Correlative measurements were also performed on individual nanoparticles, which further validate the method described here as a powerful tool to determine the extent and degree of CTAB removal from nanoparticle surfaces. This AFM-based method is broadly applicable to characterize the presence and removal of ligands from nanomaterial surfaces under hydrated conditions.