Marine environmental risk assessments rarely consider the cumulative risk from multiple contaminants and sources. Ships give rise to a range of contaminants, originating from different onboard sources, resulting in contaminant loads to the marine environment. Here, the Ship Traffic Emission Assessment Model (STEAM), in combination with the hydrodynamic and chemical fate model MAMPEC, was used to calculate loads and predicted environmental concentrations (PECs) of metals and polycyclic aromatic hydrocarbons, in four ports. PECs were compared to the predicted no effect concentrations (PNEC) to assess environmental risk from the different onboard sources, both separately and cumulatively. The results show that three out of four ports were subject to unacceptable risk. This study highlights the importance of accounting for multiple contaminant sources when assessing the marine environmental risks of shipping and challenges the suitability of the proposed new international guidelines on how to assess risk of scrubber water discharge.