This study explores the integration of nitrogen vacancies (Nv) and iron (Fe) single-atom sites into graphitic carbon nitride (g-C3N4) to enhance the performance of photo-Fenton-like reactions for wastewater treatment. Through theoretical calculations, the optimal placement of Nv and Fe sites was identified to maximize visible-light absorption and charge transfer dynamics. The integration of Nv sites, which act as electron traps, enhances electron density around Fe sites, facilitating the activation of peracetic acid (PAA) under visible light. This system demonstrates significant improvements in photocatalytic activity, achieving complete removal of bisphenol A (BPA) and 63.1% mineralization. The catalyst exhibits remarkable stability, maintaining over 80% BPA removal efficiency over 20 cycles. The study also highlights the importance of visible light in maintaining catalytic efficiency and the self-cleaning capability of the catalyst. The findings provide a theoretical foundation for designing robust single-atom catalysts for efficient wastewater treatment and other high-value applications.This study explores the integration of nitrogen vacancies (Nv) and iron (Fe) single-atom sites into graphitic carbon nitride (g-C3N4) to enhance the performance of photo-Fenton-like reactions for wastewater treatment. Through theoretical calculations, the optimal placement of Nv and Fe sites was identified to maximize visible-light absorption and charge transfer dynamics. The integration of Nv sites, which act as electron traps, enhances electron density around Fe sites, facilitating the activation of peracetic acid (PAA) under visible light. This system demonstrates significant improvements in photocatalytic activity, achieving complete removal of bisphenol A (BPA) and 63.1% mineralization. The catalyst exhibits remarkable stability, maintaining over 80% BPA removal efficiency over 20 cycles. The study also highlights the importance of visible light in maintaining catalytic efficiency and the self-cleaning capability of the catalyst. The findings provide a theoretical foundation for designing robust single-atom catalysts for efficient wastewater treatment and other high-value applications.