Ancient water supply systems provide important insights into historical sanitation practices and disease transmission patterns. This study examined soils from 2 wells of the medieval city of Phanagoria (8th–9th centuries AD) to reconstruct parasite contamination patterns during the Khazar period. Soil samples from wells 33 and 46 were analysed using light microscopy for parasite egg identification and gas chromatography–mass spectrometry (GC-MS) for faecal biomarker detection. Microscopic analysis identified 6 types of parasite eggs: Trichuris trichiura/suis, Trichuris muris, Ascaris lumbricoides/suis, trematodes of the family Brachylaimidae, Calodium hepaticum and Dibothriocephalus sp. High concentrations of parasite eggs were found in virtually all samples, indicating significant faecal contamination of the wells. GC-MS analysis revealed limited human faecal signatures but no animal biomarkers, suggesting humans as the primary contamination source. Two distinct periods of well-functioning were identified based on parasite egg distribution patterns. The findings confirm human parasitic infections in medieval Phanagoria and demonstrate the transition of these structures from wells to cisterns and finally to refuse pits. This archaeoparasitological evidence provides valuable data on medieval urban sanitation, water management practices, and parasite-host relationships in ancient Black Sea settlements.