Naphthenic Acids (NA) are important oil extraction subproducts. These chemical species are one of the leading causes of marine pollution and duct corrosion. For this reason, understanding the behavior of NAs in different saline conditions is one of the challenges in the oil industry. In this work, we simulated several naphthenic acid species and their mixtures, employing density functional theory calculations with the MST-IEFPCM continuum solvation model, to obtain the octanol–water partition coefficients, together with microsecond classical molecular dynamics. The latter consisted of pure water, low-salinity, and high-salinity environment simulations, to assess the stability of NAs aggregates and their sizes. The quantum calculations have shown that the longer chain acids are more hydrophobic, and the classical simulations corroborated: that the longer the chain, the higher the order of the aggregate. In addition, we observed that larger aggregates are stable at higher salinities for all the studied NAs. This can be one factor in the observed low-salinity-enhanced oil recovery, which is a complex phenomenon. The simulations also show that stabilizing the aggregates induced by the salinity involves a direct interplay of Na⁺ cations with the carboxylic groups of the NAs inside the aggregates. In some cases, the ion/NA organization forms a membrane-like circular structural arrangement, especially for longer chain NAs.