NMR self-diffusion and relaxation, coupled with viscosity, were used to study the properties and structure of two imidazolium-based ionic liquids, 1-ethyl-3-methylimidazolium acetate [C2MIM][OAc] and 1-ethyl-3-methylimidazolium octanoate [C2MIM][OOct]. The experimental results point to the formation of different types of aggregates in each ionic liquid. These aggregates are small and stable under flow and temperature in [C2MIM][OAc], whereas the aggregates are large and sensitive to flow and temperature in [C2MIM][OOct]. In the latter case the size of aggregates decreases both under flow and temperature increase.