The Sea Surface Microlayer (SML) is known to be enriched in trace metals relative to the underlaying water and to harbor diverse microbial communities (i.e. neuston). However, the processes linking metals and biota in the SML are not yet fully understood. In this study, we analyzed the metal (Cd, Co, Cu, Fe, Ni, Mo, V, Zn and Pb) concentrations in aerosol samples, SML (dissolved and total fractions) and in subsurface waters (SSW; dissolved fraction at ~ 1 m depth) from the Western Mediterranean Sea during a cruise in May–June 2017. The bacterial community composition and abundance in the SML and SSW, and the primary production and Chl-a in the SSW were measured simultaneously at all stations during the cruise. Residence times of particulate metals derived from aerosols deposition ranged from a couple of minutes for Co (2.7 ± 0.9 min; more affected by wind conditions) to a few hours for Cu (3.0 ± 1.9 h). Concentration of most dissolved metals in both, the SML and SSW, were well correlated with the salinity gradient and showed the characteristic eastward increase in surface waters of the Mediterranean Sea (MS). Contrarily, the total fraction of some reactive metals in the SML (i.e. Cu, Fe, Pb and Zn) showed negative trends with salinity, these trends of concentrations seem to be associate to microbial uptake. Our results suggest a toxic effect of Ni on neuston and microbiology community’s abundance of the top meter of the surface waters of the Western Mediterranean Sea.