Humic substances constitute the major organic fractions of soils, sediments and natural waters, and play a dominant role in the binding, mobilization, transport and ultimate fate of organic contaminants in subsurface systems. In this paper, two humic acid samples, Guanting and Tianjin,with different origin and chemical compositions have been investigated with AFM imaging for their adsorption and aggregation behaviors on mica. While the Tianjin humic sample is found to form small spheres with 250 to 330 nm in diameter at lower concentrations, irregular loop-chain assemblies of hundreds of nanometer in diameter with the chain width of about 40 nm are dominant for the Guanting humic sample, which may attribute to the more polar aliphatic fractions in the chemical composition in the latter. The heterogeneous and polydisperse nature of humic substances with multiple structural features, such as sponge-like structures, perforated sheets, aggregate of spheres, branches and chain-like assemblies etc., is apparent at higher concentrations for both humic samples, showing morphologically new evidence for the dominant view of the humic dual-mode sorption model. With naphthalene introduced, the assemblies of Guanting humic substances clearly become more compact with significantly narrowed branches and less porous the perforated sheet-like structures. It is indicative of that smaller nanometer scale rings present along the perforated assemblies could potentially represent hydrophobic domains, which may facilitate the adsorption and aggregation of naphthalene onto the natural particle surfaces and therefore lead to an important role of dissolved humic substances in the sorption of environmental pollutants.