This study investigates the localities of low and high F− groundwaters in the aquifer system on the flanks of Mount Meru to come up with guidelines to provide groundwater that can be used for drinking water supply without health impacts on the population. Our study focuses on parts of the flanks which were only partially or not at all covered by previous research. Results show that the groundwater chemistry of F−-rich NaHCO3 alkaline groundwater in the area is controlled by dissolution of weathering aluminosilicate minerals, dissolution of F−-bearing minerals, the precipitation of carbonate minerals as secondary products and the dissolution of magmatic gases. The low F− groundwaters which can be used for drinking water supply without health impacts under the WHO limit (1.5 mg/L) are the low-fluoride springs from the high altitude recharge areas on the eastern and north-western flanks of Mount Meru inside Arusha National Park, whereas on the western flank the groundwater meets the Tanzanian limit (4.0 mg/L). On the south-western flank, the shallow aquifer composed of alluvium deposits at lower elevations, shows F− values that meet the Tanzanian limit. One of the three investigated deep boreholes on this flank also meets the Tanzanian limit, suggesting a possibility of finding relatively low F− groundwaters in the deep aquifer. Yet, in general, the deposits at lower elevations are found to contain high to very high F− values, whereas the deposits at high elevations contain groundwater of low F− values. Thus, the internal texture and grain size of geological formations, the burial depth of these formations and the water residence times are the factors determining the groundwater mineralisation and F− concentrations in the area. The study identified that the deep hydrothermal system has influence on the high F− groundwaters on the eastern and north-eastern flanks of Mount Meru.