Recently, contamination of aquatic habitats by antibiotics, particularly tetracyclines and cancer-causing compounds, n-(n-propyl) thiourea, has caused serious concerns. The primary objective of the current investigation is to obtain an efficient method of removing these contaminants from waterbodies using the novel bimetallic heterojunction nanocatalyst supported by bentonite clay. A greener route using Psidium guajava extract reduces the precursor ions, viz., iron and gold, to Fe0 and Au0 in synthesizing composite material (Fe0+Au0@BN). The catalyst (Fe0+Au0@BN) shows a band gap energy of 1.85 eV. Nevertheless, using nanocomposite material under visible light irradiations, the photo-Fenton-like process efficiently degrades the n-(n-propyl) thiourea and tetracycline. The method enables achievement of a high degradation efficacy for both the micro-pollutants and allows very high mineralization of these pollutants, and the multiple parameters, such as pH, catalyst dosage, and H2O2 concentration, optimize the degradation process. Repeated usage of the nanocomposite material with no significant change in efficiency showed the high stability and reusability of the nanocatalyst. Furthermore, the material showed high suitability in natural water samples to decontaminate water contaminated with these two contaminants: n-(n-propyl) thiourea and tetracycline.