The eastern Baltic Sea near the Estonian coast is heavily navigated by numerous cargo ships and oil tankers. Hundreds of accidents and oil spills happen yearly in this area. Yet, there is a lack of data concerning the distribution and effects of the environmental contaminants, especially polycyclic aromatic hydrocarbons (PAHs). Different parts of the Baltic Sea have different levels of contamination; therefore a wide range of monitoring stations in coastal areas in the Gulf of Finland and Gulf of Riga were chosen. The aim of the present research was to document the responses of chosen biomarkers of environmental contaminants in different unstudied areas of the Estonian coastal sea. During 2009 and 2010 we measured PAH metabolites, EROD activities, geno- and cytotoxicity, histology, parasites and other biomarkers from the eelpout (Zoarces viviparus), a resident benthic fish species. The results showed that fish from the Gulf of Riga emitted lower levels of fluorescence in fixed wavelength analyses (representing equivalents of PAH metabolites in bile and urine), and consistently, showed less geno- and cytotoxicity and parasite infection, higher liver somatic index (LSI) and a higher condition factor (CF) than fish inhabiting areas close to the Baltic proper and in the Gulf of Finland. The results point to the effect of long-range contaminant transportation, whether atmospheric or hydrodynamic, and also to the intensive shipping activity in international routes. This study fills the gap of knowledge in this area that has persisted until now. Nevertheless, more studies in this area on the different groups of contaminants are necessary, to specify the factors that are responsible for observed biological effects.