Pollution levels of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) were investigated in the El Sol and the La Luna alpine lakes. The lakes are located in central Mexico, in the crater of the Nevado de Toluca volcano. The El Sol and the La Luna lakes are extremely relevant in Mexico and in the world because they are recognized as pristine regions and environmental reservoirs. Samples of atmospheric aerosol, sediment, plankton, and Tubifex tubifex were collected at three different sample locations for three years (2017, 2018, and 2019) at three different times of year, meaning that the weather conditions at the time of sampling were different. Pollutants were analysed by gas chromatography–mass spectrometry with negative chemical ionisation (GC-MS/NCI). Endosulfan was the most frequent and abundant pollutant, showing the highest peaks of all. Atmospheric aerosol revealed Σ2 = 45 pg/m3, including α and β, while sediment lakes displayed α, β and endosulfan sulphate as Σ3 = 1963 pg/g, whereas plankton and Tubifex tubifex showed Σ2 = 576 pg/g and 540 pg/g for α and β respectively. Results of endosulfan ratios (α/β) and (α-β/endosulfan sulphate) suggest that both fresh and old discharges continue to arrive at the lakesThis study shows for the first time the pollution levels of OCP and PCB in high mountain lakes in Mexico. These results that must be considered by policy makers to mitigate their use in the various productive activities of the region.