This work identifies Navicula permitis, freshwater diatom algae, by analyzing its 18S DNAr and testing how well it could grow and remove phenolic compounds at varying concentrations from 50 to 250 mg/L. The changes in the culture's chlorophyll fluorescence were measured when being exposed to stress. The biodegradation of phenolic compounds was tested by analyzing the enzyme activities of phenol hydroxlase and catechol dioxygenase in N. permitis. It was found that N. permitis could withstand up to 145.9 mg/L of phenol concentration. The response surface methodology was used to optimize conditions for N. permitis to degrade phenol with 50.08 mg/L of concentration, 106 cells/mL of N. permitis, and 11.38 days of treatment. Phenol removal by the Navicula permitis followed a zero-order kinetic model, and N. permitis used PHase to breakdown the pollutant. The ortho-pathway played a role in phenol metabolism. While degrading phenol, N. permitis produced biomass, which makes it a promising option for environmental remediation.