Seabird colonies influence ecosystems by releasing high concentrations of nutrients, metals, and contaminants via their wastes. Here, we examined seven lentic waterbodies impacted by two major colonies of Leach’s Storm-petrel (Hydrobates leucorhous), six from Baccalieu Island, Newfoundland and Labrador with ~ 1.95 million breeding pairs, and another from Grand Colombier Island, St. Pierre and Miquelon with ~ 200,000 breeding pairs. In comparison to nearby study sites not influenced by seabirds, we recorded more acidic pH, elevated specific conductance, and higher concentrations of dissolved organic carbon, total nitrogen, and total phosphorus in the seabird-influenced sites. The storm-petrels also significantly increased the metal concentrations of Co, Cu, Fe, Li, Nb, Ni, Sn, Sr, and Ti relative to reference sites. In the most highly affected ponds, the concentrations of Cd, Cu, and Fe exceeded Canadian Water Quality Guidelines for the Protection of Aquatic Life, implicating seabirds as biovectors of environmental contamination. Together, our data highlight the importance of seabirds, and likely other colonial organisms, as influential vectors that can strongly impact aquatic ecosystem chemistry and biota.