The area of Bagnoli (Gulf of Naples, central Tyrrhenian Sea) has been heavily exposed to pollution for over a century due to the presence of industrial sites along its coastline. The aim of this study is to analyze contaminant concentrations (i.e., heavy metals and hydrocarbons) in seabed sediments through a statistical multivariate approach. Multivariate methods permit us to describe the pollution dynamics affecting the area and distinguish between anthropogenic and natural pollution sources. Additionally, the association between contamination patterns and the wave climate characteristics of the gulf (i.e., wave period, direction, height, power, and energy) is investigated. The study confirms that the main contamination source in the Bagnoli bay is anthropogenic activities (i.e., former steel plant and sewage discharges) for the majority of investigated pollutants. It also provides evidence, however, for the potential co-existence of multiple anthropogenic and geogenic sources of arsenic and other metals that may be originating also from the water-rock interaction and submarine volcanic emissions in the Phlegraean area.