Microbial remediation is an efficient approach for improving heavy metal-contaminated water environments. Herein, this article developed a composite bacterial agent (CBA) with a high heavy metal tolerance. Within 12 h, the CBA demonstrated removal efficiencies of 65.18 ± 1.53% for As and 60.73 ± 0.94% for Hg in wastewater. This study prepared bacterial–algal fixed spheres (BAFS) to further enhance the removal efficiencies of As and Hg. Moreover, during desorption using 0.1 mol/L HNO3 for 60 min, the BAFS maintained high removal efficiencies for As and Hg after five adsorption–desorption cycles. Applying BAFS to industrial wastewater collected from factory outfall caused substantial reductions in chemical pollutants and other heavy metals. Scanning electron microscopy analysis further revealed that the internal cavities formed through the crosslinking of immobilized materials provided excellent survival carriers for bacteria and microalgae. Infrared spectroscopy analysis demonstrated the involvement of three functional groups, namely -OH, -CH2-, and C-O-C, in pollutant adsorption. Additionally, microbial community diversity analysis indicated that immobilization effectively preserved the pollutant adsorption ability of the microorganisms, increasing the abundance of functional microbial populations. These characteristics improved the efficiency of industrial wastewater treatment while promoting recycling.