The aim was to evaluate the changes in aflatoxin M1 (AFM1) and ochratoxin A (OTA) levels in human breast milk (HBM) during the first five postpartum months according to the sampling season in a cohort study from Şanlıurfa. From 78 healthy lactating mothers, HBM was taken at the 5–14 days postpartum (D5-14) and the 6th and 18th weeks postpartum (W6 and W18). Mycotoxin levels were analyzed with competitive ELISA. Generalized Estimating Equations with repeated measures (three-correlation matrix dimension) revealed a significantly higher mean AFM1 level at W6 than that on D5-14. AFM1 and OTA levels in winter and spring were considerably higher than that in summer and autumn. Maternal smoke exposure, body mass index, history of moldy food exposure, birth order, and breastfeeding type did not influence the results. Whilst season had a marked effect on the milk levels of both analytes, lactation stage affected AFM1 more notable than OTA.