The present study explores the genetic engineering of three bacterial strains, namely Pseudomonas putida, Bacillus subtilis, and also Escherichia coli, with the aim to improve their bioremediation capacities for the particular contaminants of organic origin. In order to meet the growing environmental issues, gene editing technique based on the CRISPR-Cas9 system with specific targeting was applied in the microbes selected in this study. The principle was to optimize the activity of the most important enzymes like cytochrome P450 and also dioxygenases which are responsible for the proper degradation of the organic pollutants. After genetic engineering, the microbial strains have been grown in the laboratory according to the specific condition and they were deployed to the real world where the contamination is happening. Evidence shows that the genetically engineered Pseudomonas putida performs better in bioremediation, which suggests its great potential in the complete elimination of some specific organic pollutants. The degradation of the pollutants during the B. subtilis growth was advanced and featured pathway specificities, highlighting this natural species potential for the development of the targeted bioremediation. Study of the mRNA expression patterns for the genetically modified E. coli gave some hints about the mechanisms that result in the enhanced organic pollutant degradation in E. coli.