<p>Polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) are growing organic and inorganic pollutants in blue ecosystems due to increasing maritime traffic, industrial effluents, and other anthropogenic activities. Over the last two decades, microbial remediation has emerged as a sustainable strategy for mitigating PAHs and HMs. However, the co-occurrence of PAHs and HMs presents considerable challenges to microbial degradation, as HMs can interfere with PAH-degrading enzymatic pathways. Interestingly, sub-inhibitory concentrations of certain HMs may induce adaptive microbial responses, including enhanced biofilm formation, extracellular polymeric substance production, and activation of stress-response mechanisms. This review highlights recent advances in microbial bioremediation strategies targeting PAH–HM co-contamination. Advanced kinetic models and molecular insights reveal complex interactions, highlighting the need to optimize microbial strategies for co-contaminated site remediation. Innovative approaches such as CRISPR-Cas-based gene editing are being employed to enhance microbial resistance and catabolic efficiency. In addition, algae–microbe consortia and biofilm-based systems offer synergistic potential in marine environments. Emerging tools including electro-bioremediation, metagenomics, and artificial intelligence (AI)-driven monitoring systems are contributing to a deeper understanding of in situ microbial functions and enabling real-time optimization of remediation processes. These integrative strategies not only improve pollutant removal efficiency but also align with sustainable and scalable aquatic pollution management practices. The convergence of environmental microbiology, synthetic biology, and digital technologies offers a transformative framework to tackle complex pollutant mixtures and supports global sustainable development goals (SDG 6-clean water and sanitation).</p> Graphical Abstract <p></p>