The Santiago-Guadalajara River Basin (SGRB), located in western Mexico, is one of the most polluted rivers in the country. A pesticide monitoring program was carried out from January 2022 to September 2022, during which time water samples collected at 25 sites in the main stem and tributaries revealed the presence of 13 of the 24 pesticides analyzed, including α-BHC, β-BHC, γ-BHC (Lindane), γ-Chlordane, Hexachlorobenzene, Heptachlor, Aldrin, α-Endosulfan, DDT, -4,4, Methoxychlor, Chlorpyrifos-methyl, Endosulfan sulfate, and Dicofol. A high level of correlation was found between the identified pesticides, which could mean that several of these pesticides reached a stable level within the monitored water bodies. Most of the identified pesticides are classified as high environmental risk according to the Stockholm Convention because of their persistence and high degree of toxicity to the environment and human health. A Pesticide Toxicity Index (PTI) was applied to identify the streams considered to be of concern due to the presence of pesticides exceeding the threshold limits established by national and international guidelines. Performing a calculation for the entire Santiago-Guadalajara River Basin, the PTI reached a value of 0.833, which, according to the criteria of this method, classifies it as a “Moderate” level of risk for aquatic life. Increased regulatory and surveillance measures by state and federal authorities are required to prevent the use of these pesticides, which have been restricted globally.