The Morroa aquifer, which is an essential source of water supply in Sucre, Colombia, with more than 500,000 users, may be at risk because of pesticide contamination that comes from different agricultural activities. The aim of this research was to evaluate the relationship between the presence of pesticides and the physicochemical properties of soils in the most vulnerable areas of the Morroa aquifer. Therefore, farmers were surveyed about pesticide usage and soil samples which were taken for analysis of pesticide and physicochemical properties. The results demonstrated that soils in these areas were relatively homogeneous in terms of texture, pH, cation exchange capacity and organic matter content. Pesticides detected in these soils were malathion, β-BCH, p-p’DDE, m-p’DDD, p-p’DDT, endosulfan, endrincetone, chlorpyrifos, dieldrin, endosulfan-sulfate, heptachlor-epoxide, and parathion. Physicochemical properties such as pH and texture of soils and intrinsic characteristics of the pesticide were found as the most influential variables according to statistical results. This study also presents a map of the spatial distribution of pesticide concentration according to the concentration of pesticides, which constitutes an important tool for the planning of agricultural activities that supports decision-making and the implementation of measures to mitigate potential impacts caused by pesticide pollution.