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This study investigated the basement aquifer beneath the urbanised city of Niamey and the agricultural fields of Kollo, SW of Niger. During the observation period spanning from 2021 to 2023, groundwater and surface water samples were collected for analysis of major ions and the stable isotopes oxygen-18 and deuterium (δ18O and δ2H) of water. To trace the origin of high nitrate concentrations (NO3−) found in several observation and drinking water wells in both areas, δ15N and δ18O isotope values of NO3− were analysed in groundwater and eluted soil samples. The observed hydrochemical patterns mainly reflect the heterogeneity of the weathered fringe of the basement aquifer. Decreasing concentrations of NO3− and δ18O and δ2H values were observed in relation to the distance of the Niger River and increasing thickness of the clay layer on the surface. The wells close to the river in Niamey show a dilution effect during the flood season, and the NO3− concentrations displayed a continuous increasing trend. The δ15N-NO3 and δ18O-NO3 values confirmed that septic tank water is spreading in the region of Niamey and that manure originating from livestock in Kollo is the main source of NO3−. The patterns of δ15N in the soil samples coincide with those of cattle's manure spread in both areas. The shallow wells show significantly higher values of electric conductivity and NO3− concentrations compared to the deeper wells, which clearly indicates the influence of shallow septic tanks on water quality. [ABSTRACT FROM AUTHOR]