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Water quality assessment for river systems is important for tracing any changes in quality caused by, among other things, mining activities. Mining activities can be one of the most impactful sources of water contamination. In Malawi, gold deposits occur in the basement rocks of the Lisungwi-Manondo region. As a result, a boom in small scale artisanal mining has occurred as residents have settled in the area. Despite the development of artisanal small scale mining activities, few studies have investigated the water quality of the main rivers in the region (i.e., the Lisungwi and Kaphamtengo Rivers), upon which local residents are highly dependent for daily use. This study provides baseline data for water quality in the region. On-site and laboratory measurements were carried out on the river water samples, to obtain the physio characteristics (e.g. pH, turbidity, electric conductivity) and the major and minor element concentrations of the river water. The data was compared to the regional geology to establish anthropogenic and/or geological impacts on the water quality. The river water has a moderate buffering capacity due to its high alkalinity, along with high Ca, Si, Mg, and Cl concentrations sourced from the gneiss and calcsilicate rocks in the region. Further analysis of the water quality based on the physiochemical parameters, major and trace element concentrations, showed that the river waters were in accordance with guidelines set by the Malawi Bureau of Standards (MBS) and the World Health Organization (WHO) for river water quality, with all analyzed parameters being below the stipulated standards. Our results indicated that the regional geology exerts a significant control on water chemistry, but the mining activities on and along the river water leaves the water in an uncontaminated state.