The aim of this study was to assess the levels of some persistent organic pollutants in the surface sediments from the Zahuapan and Atoyac rivers (Tlaxcala, Mexico), as well as to determine the genotoxic potential, by the micronucleus test in Vicia faba, of the sediments and agricultural soils irrigated with water from these rivers. This document is the first study on the presence of POPs in surface sediments of the above-mentioned rivers; among the compounds analyzed are the HCH isomers, DDT and its metabolite DDE, HCB, mirex, aldrin, and 41 PCB congeners. The concentrations of HCB, DDTs, HCHs, and PCBs ranged from 138-510, 45-450, 3-27, and 59-1876 μg kg −1 dry weight, respectively. The highest levels of HCB, HCH isomers, and PCB congeners were found in the Atoyac River, and these compounds have the potential for causing an environmental impact. On the other hand, biological testing shows that both sediments and agricultural soils possess a genotoxic potential, given that the micronuclei frequency in V. faba is increased.