Structural organization of hydrogen and oxygen functionalized nanodiamond (ND) particles in hydrosols was investigated using a cryo-TEM method. The formation of chain-like structures was observed for hydrogen functionalized NDs while oxygen functionalized NDs tend to form more compact structures. In order to understand possible interaction mechanisms between NDs in hydrosols and to explain these experimental results, first-principles calculations were performed. Charged H-terminated ND particles and particles with partially dissociated hydroxyl and carboxyl groups on the surface were investigated as models of a real ND particle in solution. For positively charged H-terminated particles, it was established that charge distribution is determined by the values of valence band maximum for the particle facets. For negatively charged oxygen functionalized particles, the charge is localized near functional groups. In both cases, interaction is determined by the interplay between Coulomb interaction and van der Waals attraction. For detailed analysis of the ND interaction, the continual model considering this interplay was developed. The results obtained with this model indicate that the formation of chain structures from linked ND particles is caused by charge separation inside the ND particle. For the H-terminated ND particles in water solution, strongly anisotropic distribution of electrostatic potential around the particles promotes formation of non-compact chain structures of particles via interaction between facets with opposite charges. This effect of charge separation is lower in the oxygen functionalized particles as the charge is localized at the uniformly distributed O-containing functional groups, thus, more compact structures can be formed. These general qualitative statements address the problem of interactions between the large number of ND particles and explain the presented cryo-TEM experimental results.