The release of different hazardous substances into the water bodies during the industrial and textile processing stages is a serious problem in recent decades. This study focuses on the potentiality of Fe3O4-NPs-based polymer in sustainable bioremediation of toxic substances from contaminated water. The biosynthesis of Fe3O4-NPs by A. tamarii was performed for the first time. The effect of different independent variables on the Fe3O4-NPs production were optimized using Plackett–Burman design and central composite design (CCD) of Response Surface Methodology. The optimum Fe3O4-NPs production was determined using incubation period (24 h), temperature (30 °C), pH (12), stirring speed (100 rpm) and stirring time (1 h). The incorporation of Fe3O4-NPs into chitosan beads was successfully performed using sol–gel method. The modified nanocomposite exhibited remarkable removal capability with improved stability and regeneration, compared to control beads. The optimal decolorization was 94.7% at 1.5 g/l after 90 min of treatment process. The reusability of biosorbent beads displayed 75.35% decolorization after the 7th cycle. The results showed a highly significant reduction of physico-chemical parameters (pH, TDS, TSS, COD, EC, and PO4) of contaminated wastewater. The sorption trials marked Fe3O4-NPs-based biopolymer as efficient and sustainable biosorbent for the elimination of hazardous toxic pollutants of wastewater in a high-speed rate.