Atmospheric emissions related to harbor-related activities can significantly contribute to air pollution of coastal urban areas and so, could have implications to the citizens’ health that live in those areas. Of great concern is the local impact of the emissions that are generated while ships are at berth, since not all types of ships switch off the main engines. This paper intends to investigate the influence of the stack configuration for generic cargo ships on the exhaust smoke dispersion, using the Port of Leixões as a case study and a series of wind tunnel experiments with support of Particle Image Velocimetry (PIV) technique. For that, different configurations of the stack of a cargo ship (in terms of height, geometry and diameter) were simulated under the typical wind conditions of the study area. The PIV results indicate negligible differences between the medium and long stack height, with the short stack height presenting a strong impact on the flow field around the stack. For the short stack height, the flow field is not only disturbed by the stack, but also by the cargo ship bridge, with both obstacles promoting disturbances on the flow field and creating a large wake turbulence effect, which is important for the downwash phenomena. Regarding the effects linked with two distinct geometries (straight or curved), the results show that the straight chimney led to higher perturbation of wind field when compared with the curved geometry. The curved stack presents an increase of vorticity, indicating the generation of more turbulent structures. The PIV results also confirmed that higher wind velocity at the inlet conducts to higher vorticity levels, as well as a higher number of Kelvin–Helmholtz structures. For distinct wind conditions the PIV measurements point out different patterns, indicating the northern wind direction as the most favorable condition for the exposure of dock workers to pollutants. Overall, the results showed that a ship stack with a curved end, medium length and smaller diameter has the capability to promote the behaviors in the flow that are coherent with increased pollutant dispersion.