Harbours are important hubs for economic growth in both tourism and commercial activities. They are also an environmental burden being a source of atmospheric pollution often localized near cities and industrial complexes. The aim of this study is to quantify the relative contribution of maritime traffic and harbour activities to atmospheric pollutant concentration in the Venice lagoon. The impact of ship traffic was quantified on various pollutants that are not directly included in the current European legislation for shipping emission reduction: (i) gaseous and particulate PAHs; (ii) metals in PM10; and (iii) PM10 and PM2.5. All contributions were correlated with the tonnage of ships during the sampling periods and results were used to evaluate the impact of the European Directive 2005/33/EC on air quality in Venice comparing measurements taken before and after the application of the Directive (year 2010). The outcomes suggest that legislation on ship traffic, which focused on the issue of the emissions of sulphur oxides, could be an efficient method also to reduce the impact of shipping on primary particulate matter concentration; on the other hand, we did not observe a significant reduction in the contribution of ship traffic and harbour activities to particulate PAHs and metals. [Figure not available: see fulltext.]