The sharp increase in waterborne diseases due to bacterial contamination is limiting the supply of safe water in developing countries. This study focuses on the development and optimization of a low‐cost ceramic membrane based on natural resources and local waste for eliminating bacteria from water. The augmented simplex centroïd mixture design (ASCD) was used. The obtained optimal formulation consisted of 65% Ebebda clay (EB) 18.64% Koutaba clay (KG), and 16.34% cassava peel (PM) with a holding temperature of 1 100°C. The raw materials and membrane were characterized by chemical analysis using X‐ray florescence, X‐ray diffractometry, Thermal Gravimetric/Differential Scanning Calorimetry (TG/DSC), FTIR, scanning electron microscopy, SBET, porosity and flexural strength. The optimal membrane has 43.26% of porosity, 7.46 MPa of strength, 0.55 m2/g of specific surface area, an average pore diameter of 1.31 µm and a water permeability of 4 345,87 L h−1 m−2 bar−1. The ability of the membrane support to retain Pseudomonas aeruginosa, Klebsiella pneumoniae, Salmonella sp and Staphylococcus aureus bacteria present in contaminated water was finally assessed. Retention tests showed 100% of P. aeruginosa, 97.37% of K. pneumoniae, 93.69% of Salmonella sp, and 90% of S. aureus, making this new, less expensive ceramic membrane a potential candidate for the water treatment.