Fluoride contamination in water sources is a global concern due to its adverse health effects. Traditional methods of fluoride removal often involve chemical treatments, which can be costly and environmentally harmful. In recent years, microbial remediation has emerged as a promising alternative, leveraging the natural capabilities of microorganisms to adsorb fluoride ions from water. This utilizes various microorganisms such as bacteria, fungi, and algae. This chapter explores the mechanisms of microbial fluoride remediation, including biological adsorption, bioaccumulation, bioprecipitation, biomineralization, and enzymatic degradation. Factors affecting microbial remediation efficiency, such as pH, temperature, nutrient availability, and fluoride concentration, are discussed. While microbial remediation offers advantages over traditional methods, it also faces limitations, including substrate specificity and scalability challenges. Innovative approaches, including genetic engineering, biofilm technology, nanotechnology, and bioreactor design, hold promise for overcoming these limitations and enhancing remediation efficiency. Future research directions focus on discovering novel microbial strains with enhanced fluoride removal capabilities, optimizing process conditions, and integrating microbial remediation with other treatment modalities for synergistic effects. By addressing these challenges and advancing research in microbial remediation, we aim to develop holistic and sustainable solutions for combating fluoride contamination in water resources.