A field operable surface enhanced Raman scattering (SERS) sensor system was applied for the first time under real conditions for the detection of polycyclic aromatic hydrocarbons (PAHs) as markers for petroleum hydrocarbons in the Gulf of Gdańsk (Baltic Sea). At six stations, seawater samples were taken, and the sensor system was applied in situ simultaneously. These measurements were compared to the results of conventional GC/MS laboratory analysis of the PAH concentrations in the seawater samples. For a PAH concentration above 150ng(12PAH)l⁻¹, there was agreement between the SERS sensor and the GC/MS determinations. A standard addition experiment yielded a PAH concentration of 900ngl⁻¹ at the Gdańsk Harbor, which was of the same order as the GC/MS determinations of 12PAHs (200ng(12PAH)l⁻¹). The high SERS detection limit for seawater samples is explained by the competition for PAHs between the sensor membrane and particulate matter surfaces. Thus, the SERS sensor can be applied, e.g., as a non-quantitative alarm sensor for relatively high PAH concentrations in heavily polluted waters. The spectral unmixing procedure applied for Gdańsk Harbor water confirmed the presence of phenanthrene at the highest concentration ([Phe]=140ngl⁻¹) and of Chr (2.7ngl⁻¹), but it did not detect the other PAHs present in the Gdańsk Harbor water, as determined by GC/MS. When compared to the past literature and databases, the SERS spectra indicated the presence of a mixture of molecules consisting of carotenoids, n-alkanes, amines or fatty acids, and benzimidazoles at the coastal station ZN2. The spectra in the offshore direction indicated carboxylic acids. Interpretation of the farthest offshore in situ SERS measurements is difficult, principally due to the limited availability of reference spectra. The detection of the lower PAH concentrations commonly found in Baltic coastal water needs further research and development to obtain better sensitivity of the SERS sensor. However, the high analytical specificity of the SERS sensor also allows the detection of other chemical species that require the development of a SERS/Raman library for specific in situ spectral interpretation.