The increasing demand for water resources and sustainable water supply planning have sparked interest in reusing produced water, offering economic, social, and environmental benefits, especially in water-scarce regions. Genome editing technologies are revolutionizing wastewater treatment, removing contaminants, heavy metals, and hydrocarbons, benefiting water environmental fields and attracting increased interest in the oil and gas industry. Genome editing techniques may lead to the development of microbial bioremediation technologies, crucial for controlling environmental pollution in aquatic environments, despite challenges posed by variable and stressed environments. Genomic engineering techniques optimize microbial metabolic pathways and enhance enzymatic activities, but rely on selectable markers like herbicide, anti-metabolite, and antibiotic resistance genes (ARGs), posing environmental risks . This paper explores the use of TALEN, ZFNs, and especially CRISPR Cas9 as gene editing tools for wastewater bioremediation, focusing on specific microbes. The CRISPR technique enhances genome editing efficacy, versatilities, and orthogonalities by complementing targeted sequences with gRNA and associated protein’s endonuclease activities. CRISPR techniques are not yet widely used in the field of water environment microbiology due to its complexity, heterogeneity, and variability. CRISPR technologies may bring breakthroughs in environmental microbial technologies, but future efforts must minimize off-target cleavage, expand PAM recognition, and mitigate gene release risks. This review highlights the practical application of CRISPR techniques in water environmental microbiological processes, including microbial community balance engineering, wastewater treatment system optimization, and selective pollutant-to-chemical bioconversion.