The interactions between gold nanoparticles, their surface ligands and the solvent critically influence the properties of these nanoparticles. Although spectroscopic and scattering techniques have been used to investigate their ensemble structure, a comprehensive understanding of these processes at the nanoscale remains challenging. Electron microscopy makes it possible to characterize the local structure and composition but is limited by insufficient contrast, electron beam sensitivity and the requirement for ultrahigh-vacuum conditions, which prevent the investigation of dynamic aspects. Here we show that, by exploiting high-quality graphene liquid cells, we can overcome these limitations and investigate the structure of the ligand shell around gold nanoparticles and at the ligand–gold interface in a liquid environment. Using this graphene liquid cell, we visualize the anisotropy, composition and dynamics of ligand distribution on gold nanorod surfaces. Our results indicate a micellar model for surfactant organization. This work provides a reliable and direct visualization of ligand distribution around colloidal nanoparticles.