Understanding the dynamics of sorption and desorption is essential for assessing the persistence and mobility of pesticides. These processes continue to influence ecological outcomes even after pesticide use has ended, as demonstrated by our study on dimethoate behavior in distinct soil samples from Croatia, including coastal, lowland, and mountainous regions. This study focuses on the sorption/desorption behavior of dimethoate in soil, explores the relationship between its molecular structure and the properties of soil organic and inorganic matter, and evaluates the mechanisms of the sorption/desorption process. The behavior of dimethoate was analyzed using a batch method, and the results were modeled using nonlinear equilibrium models: Freundlich, Langmuir, and Temkin models. Soils with a higher organic matter content, especially total organic carbon (TOC), showed a better sorption capacity compared to soils with a lower TOC. This is probably due to the less flexible structures in the glassy phase, which, unlike the rubbery phase in high TOC soils, do not allow dynamic and flexible binding of dimethoate within the organic matter. The differences between the H/C and O/C ratios indicate that in high TOC soils, flexible aliphatic compounds, typical of a rubbery phase, retain dimethoate more effectively, whereas a higher content of oxygen-containing functional groups in low TOC soils provides strong association. The lettered soils showed stronger retention of dimethoate through interactions with clay minerals and metal cations such as Mg2+, suggesting that clay plays a significantly more important role in enhancing dimethoate sorption than organic matter. These results highlight the importance of organic matter, clay, and metal ions in the retention of dimethoate in soil, indicating the need for remediation methods for those pesticides that, although banned, have had a long history of use.