The Santiago River near the Guadalajara Metropolitan Area is one of the most contaminated water bodies in Mexico, where heavy metals pose a major threat to aquatic ecosystems. Chronic metal pollution has promoted the adaptation of native microbial communities, including the production of metal-chelating metabolites such as siderophores, which represent a valuable resource for remediation-oriented biomaterials. In this study, bacterial strains were isolated from water and sediment samples, then screened for siderophore production using the Chrome Azurol S assay (CAS), complemented by a MATLAB-based image processing approach for semi-quantitative ranking prior to taxonomic identification by MALDI-TOF MS. Based on biosafety considerations and cultivation robustness, Bacillus thuringiensis was selected as a benchmark case, being immobilized onto activated carbon to produce a carbon–bacteria biocomposite (CBM). To evaluate the performance of CBM, Cu(II) was used as a model contaminant due to its industrial relevance, persistence, toxicity, and strong complexation behavior. Batch adsorption experiments showed that the CBM exhibited a 23.9% higher maximum Cu(II) sorption capacity than pristine activated carbon. Acute toxicity assays using Vibrio fischeri further indicated reduced toxicity in CBM-treated effluents, supporting the feasibility of this contained biocomposite for heavy metal remediation.