Pesticides in soils raise concerns about the biodiversity, food safety, and contamination of watercourses, contributing to unsustainable land management practices. Monitoring the residue levels in agricultural soils is essential, as this offers valuable insights into the current extent of soil contamination and potential environmental risks attributed to their application. This study aimed to address the occurrence of the currently used herbicides in soil under intensive crop production, comparing the results of monitoring at two depths (0–30 and 30–60 cm) in 2013 and 2023. The research concerned the main agricultural area in Vojvodina Province (Serbia) and evaluated the presence of 41 herbicides in 128 localities. Pesticides were found in all samples, finding even more than six different herbicides per sample. The significant concentrations of s-metolachlor, etofumesate, clomazone, diflufenican, pendimethalin, and terbuthylazine found can be attributed to application practices, as they are typically applied pre-emergence, either through direct soil treatment with or without incorporation. Moreover, the correlation between different depths, herbicide residues, and soil properties was not significant. The decrease in the herbicide residues found in 2023 compared to the residues found in 2013 can be attributed to the implementation of good agricultural practices, which promote sustainable agricultural strategies through controlled pesticide application.