Co-contamination of polycyclic aromatic hydrocarbons (PAHs) with heavy metals (HMs) in aquatic environments is a global threat; however, little is understood about PAH biodegradation in these sites. In this study, PAHs' biodegradation in the presence of HMs in water by a metal-tolerant consortium composed of Bacillus subtilis and fungus Acremonium sp. was investigated. The consortium demonstrated higher tolerance to the tested HMs (Fe2+, Al3+, Ni2+, Cu2+, Mn2+ and Zn2+) than the individual consortium components, and the tolerance to individual metals decreased with increasing metal concentrations. In the absence of HMs in aquatic systems, the consortium efficiently degraded naphthalene, fluorine, phenanthrene, anthracene and fluoranthene individually (50 mmol/L) over 10 days. However, while Ni2+ supplementation (5 mmol/L) suppressed phenanthrene and anthracene removal (p ≤ 0.01), enhanced fluoranthene degradation relative to the control was observed. Cu2+, Zn2+, Fe2+ and Al3+ supplementation demonstrated significant inhibition against individual phenanthrene, anthracene and fluoranthene removal, and Cu2+ showed a more significant effect on the degradation of these PAH compounds compared to other metals. Conversely, Mn2+ significantly enhanced the removal of fluorene, phenanthrene and fluoranthene, but inhibited anthracene degradation. HM contamination in aquatic systems did not show any effect on naphthalene bioremediation, possible due to its rapid degradation over a short time. Thus, metals affect PAH aquatic biodegradation by consortia, depending on metal species and PAH compound, underlining the complex nature of co-contaminated systems containing HMs and PAHs. To our knowledge, this is the first study to examine the influence of HMs on PAHs' bioremediation by such PAH-degrading consortia in water.