Copper (Cu) has a narrow range between optimal concentrations as a micronutrient critical for phytoplankton growth and concentrations potentially toxic to living organisms. This sensitivity indicates an ecosystem vulnerability that threatens not only nature but also human health due to bioaccumulation. An important source of elevated Cu concentrations in coastal environments are biocides used as antifouling protection on ships. A pilot study conducted in the Marine Protected Area (MPA) of the Krka Estuary (Croatia) over a period of 16 months investigated the relationship between ship traffic and Cu concentrations. The aim was to contribute to more informed environmental management by assessing the associated risks. In the study presented here, Cu concentrations were monitored, analyzed, and correlated with vessel traffic. Observations revealed that the seasonal increase in maritime traffic caused by nautical tourism was associated with an increase in Cu concentrations of more than five times, posing a toxicity risk to the environment. In order to understand the distribution of copper emissions, a mapping of maritime traffic was carried out by counting transits, radar imagery, and drone photography. This approach has proven sufficient to identify the potential risks to the marine environment and human health, thus providing an effective assessment tool for marine stakeholders.