The use of pesticides in Mexican agriculture creates an interest in learning about the presence of these substances in different environmental matrices. Glyphosate (GLY) is an herbicide widely used in the state of Campeche, located in the Mayan zone in the western Yucatan peninsula. Despite the fact that GLY is considered a non-toxic pesticide to humans, its presence in water bodies through spillage, runoff, and leaching are a risk to human health or biota that inhabit these ecosystems. In the present study, glyphosate residues were determined in groundwater, bottled drinking water, and the urine of subsistence farmers from various localities of the Hopelchén municipality in Campeche. Determination of GLY was carried out using Enzyme-Linked Immunosorbent Assay (ELISA). The highest concentrations of GLY were observed in the groundwater (1.42 μg/L) of Ich-Ek and urine (0.47 μg/L) samples of subsistence farmers from the Francisco J. Mújica communities. The glyphosate concentrations in groundwater and bottled drinking water indicate an exposure and excessive use of glyphosate in these agricultural communities. This is one of the first studies that reports glyphosate concentration levels in human urine and bottled drinking water in México and in the groundwater in the Yucatan Peninsula as part of a prospective pilot study, to which a follow-up will be performed to monitor this trend over time.