The aggregation behavior of asphaltene in aqueous solution is systematically investigated based on a classical molecular dynamics study. In this work, a novel approach is adopted in order to investigate the structural and dynamical properties of the asphaltene nanoaggregates using different water models. The end-to-end distance of the asphaltene molecule is probed in order to understand the aggregation behavior in aqueous solution. The accuracy of different water models, that is, simple point charge, TIP4P-D, and TIP5P, is thoroughly investigated. In order to probe the dynamical properties of the asphaltene nanoaggregates, the transport coefficients, namely, diffusion coefficient and shear viscosity, are computed. The obtained results highlight the importance of using the appropriate water model in order to accurately study the aggregation behavior of asphaltene in aqueous solution.