Mobility is a key feature affecting the environmental fate, which is of particular importance in the case of persistent organic pollutants (POPs) and emerging pollutants (EPs). In this study, the global mobility classification artificial neural networks-based models employing GC retention times (RT) and 2D molecular descriptors were constructed and validated. The high usability of RT was confirmed based on the feature selection step performed using the multivariate adaptive regression splines (MARS) tool. Although RT was found to be the most important, according to Kruskal-Wallis ANOVA analysis, it is insufficient to build a robust model, which justifies the need to expand the input layer with 2D descriptors. Therefore the following molecular descriptors: MPC10, WTPT-2, AATS8s, minaaCH, GATS7c, RotBtFrac, ATSC7v and ATSC1p, which were characterized by a high predicting potential were used to improve the classification performance. As a result of machine learning procedure ten of the most accurate neural networks were selected. The external validation showed that the final models are characterized by a high general accuracy score (85.71–96.43%). The high predicting abilities were also confirmed by the micro-averaged Matthews correlation coefficient (MAMCC) (0.73–0.88). To evaluate the applicability of the models, new retention times of selected POPs and EPs including pesticides, polycyclic aromatic hydrocarbons, pharmaceuticals, fragrances and personal care products were measured and used for mobility prediction. Further, the classifiers were used for photodegradation and chlorination products of two popular sunscreen agents, 2-ethyl-hexyl-4-methoxycinnamate and 2-ethylhexyl 4-(dimethylamino)benzoate.