Background: Nitrate is a water pollutant widely disseminated and has been linked to health disorders, including thyroid disorders as subclinical hypothyroidism. Methods: A familial, observational, descriptive, and cross-sectional study was conducted on individuals in rural areas of Durango, Mexico. The sample comprised 102 subjects forming part of 26 families’ resident in the abovementioned areas. All those fulfilling the inclusion criteria were tested for exposure biomarkers (plasma and urinary nitrite), an effect biomarker (percentage of methemoglobin), and thyroid function (thyroid profile). The genotypes corresponding to the single nucleotide polymorphisms (SNPs) rs965513 and rs1867277 of the FOXE1 gene were also determined. The presence of anti-thyroid peroxidase antibody (TPO-Ab) was determined in those subjects who were found to have subclinical hypothyroidism. The variables of interest comprised the subject’s age, sex, body mass index (BMI), and thyroid profile, as well as the exposure and effect biomarkers, and the levels of nitrate exposure via drinking water. Pearson's correlation, principal component analysis (PCA), heatmap and cluster analysis as well as post hoc Kruskal-Wallis and chi-squared were performed. Results: 102 individuals were analyzed, 45% presented subclinical hypothyroidism, a negative correlation was observed between methemoglobin and total T3 (r= -0.43, r2=18.49, p=0.001) and free T3 levels (r= -0.34, r2=11.56, p=0.001); also between plasma nitrite and free T4 (r= -0.20, r2= 4, p=0.045) and total T3 (r= 0.23, r2= 5.29, p=0.022). Only 15.7% had positive antithyroid ab-TPO, while the polymorphic genotype (AA) represent only 3% (rs965513) and 4% (rs1867277) among subclinical hypothyroidism. Conclusions: The subclinical hypothyroidism in the population studied is mainly due to nitrate contamination in drinking water.