The Buenavista landfill is located east of the city of Medellín, but it has a slope steeper than 30% and is less than 600 m away from the Piedras River, possibly influencing the quality of the drinking water in the city. Many complex residues are disposed of in this landfill, including pharmaceuticals and personal care products (PPCPs) such as levonorgestrel (LNG), which may reach water bodies via runoff and leaching. We assessed the levels of LNG in the effluent of an upflow anaerobic sludge blanket (UASB) reactor from the Buenavista landfill by uHPLC–DAD, as well as the endocrine disruptor effect of LNG on placental cell lines (BeWo) and human sperm cells. Additionally, the potential leaching of LNG was assayed under laboratory conditions using soil layers that were sampled from the Buenavista landfill. LNG was detected at levels of 315 μg·L−1 in the effluents of the UASB reactor. Thus, the UASB reactor is not an efficient treatment method for the removal of recalcitrant pollutants. Additionally, we found that a layer of soil used as a cover material may adsorb more than 90% of LNG pollutants, but small amounts may still be leached, which means that a cover material is not a strong enough barrier to fully prevent the leaching of LNG. Finally, our results show that the leachate fraction decreased the levels of β-human chorionic gonadotropin, but not sperm motility or viability. Thus, leached LNG could trigger reproduction disorders, but further studies should be carried out to investigate its potential effects in more detail.