CYANOBACTERIA in drinking water are a major problem that threatens humans, animals and plants, especially if they produce toxins.This study aimed to remove cyanobacterial species, especially Merismopedia mianima and their microcystins (MCs) during the treatment process of drinking water. Water samples were collected from raw water, after each process and from the final treated water including coagulation, sedimentation, filtration and disinfection as well as from the final treated during the study period (May–December 2019). In all of these samples, M. minima was detected with an average cell count of 80-2200 cells/ mL.This increase in algal count may be due to the warm season when the temperature was favorable for cyanobacterial growth (blooming). Results also showed that traditional treatment methods could remove some cyanobacterial species but are ineffective in for completely removing MCs produced by M. minima, which was isolated even from the final stage of drinking water treatment. Furthermore, MCs were determined by High-Performance Liquid Chromatography (HPLC) analysis and the particulate MCs concentration of M. minima was found to record 500μg MCs/L (2.27pg/cell). Extracellularly released MCs were also not completely removed and remained at high concentrations of 0.74–1.47μg/L which exceeded the limit proposed by the World Health Organization (WHO= 1μg/L).The toxin concentration was mitigated to levels less than WHO limits when water sediments were used to remove MCs. Therefore, this study recommends using sediments to remove cyanobacteria and their cyanotoxins from water plants, which is an inexpensive method especially for the developing countries.