Abstract The high prevalence of dental fluorosis and bone mineralization deficiency as a result of exposure to fluorides has increased in Kenya over the years due to consumption of water with elevated levels of fluoride. The World Health Organization (WHO) provides a guideline of 1.5 mg/L level of fluoride in drinking water. However, majority of studies carried out in Kenya over the last 40 plus years have indicated very high levels of fluoride in drinking water in various regions, with a prevalence in dental fluorosis observed in children and adults living in Rift valley and central regions due to basaltic and volcanic rocks. Unfortunately, this trend of fluoride-induced enamel changes has been observed in other regions such as Nairobi and Machakos which were originally presumed to contain low fluoride levels. This study sought to analyse the applicability of Maerua subcordata root powder (MSRP) in the removal of fluorides in borehole drinking water. Fresh Maerua subcordata roots were peeled to obtain the white flesh, chopped into small pieces, dried and ground into powder. The process parameters varied were; fluoride ion concentration [F−] (0–12 mg/L), adsorbent dosage (0–200 g/L) and equilibration time (30–240 min) [F−] were hence analysed before and after treatment using ion selective electrode (ISE) fluoride meter. Results indicated that MSRP is a viable plant in fluoride treatment with approximately 68% fluoride ion removal efficiency. An MSRP dosage of 200 g/L was found optimal in [F−] reduction while a 2 mg/L [F−] concentration recorded the highest reduction of [F−]. The optimal equilibration time was found to be 30 min. The results can be used to develop a low-cost column for treatment of high fluoride waters in rural areas using MSRP. Borehole samples were treated with MSRP using the optimized conditions; however their reduction levels were lower than the [F−] standards used. It is envisaged that with further modification and/or doping with zero-valent iron nanoparticles, it’s efficiency will be improved.