The Nigerien Liptako in southwest Niger has gold mineralisations in Birimian formations (Paleoproterozoic) that have been mined for several decades. The objective of this study was to document the concentrations of arsenic and other toxic trace elements in groundwaters, river waters, suspended particulate matter and sediments and discuss the potential influence of artisanal gold mining on arsenic and trace elements enrichment. For this, forty-three groundwater samples (boreholes and wells) were analysed in mined and unmined areas. Surface waters, suspended particulate matters and sediments were sampled in three rivers at stations upstream and downstream from mining sites. Rock samples extracted from mine galleries were collected for mineralogical and geochemical characterization. In groundwater, arsenic concentrations ranged from 0.018 to 202 µg/L, exceeding drinking water guidelines (10 µg/L) in three artisanal gold mining areas. Manganese exhibited concentrations exceeding the potability limit in 23% of the samples, mainly in the Continental Terminal aquifer. In rivers, arsenic was the element most enriched in suspended particulate matter and sediments, but its concentration in water did not exceed 3 µg/L. Mineralogical analysis of rocks showed traces of arsenic in association with iron oxides, suggesting a release of arsenic in groundwater by desorption. The consumption of these waters rich in arsenic or manganese presents serious risks for health. These data represent the first large-scale investigation of arsenic and trace elements concentrations in groundwaters and surface waters in the Nigerien Liptako, where no or very scarce water quality measurements have been published yet.