High-resolution GC/MS with electron impact (EI) and selected ion recording (SIR), after a nondestructive sample extraction and cleanup using semipermeable polyethylene membrane (SPM), and further HPLC fractionation on activated carbon column were applied to determine polychlorinated naphthalenes (PCNs) in a pelagic food web including mixed subsurface plankton, Baltic herring (Clupea harengus), and harbour porpoise (Phocoena phocoena). Nearly all theoretically possible tetra- through heptachlorine substituted naphthalene congeners were identified and quantified in all samples examined. The concentrations, profile, and patterns of PCNs found in spatially different plankton samples indicate the atmosphere as a dominating long-range transportation and deposition route of these pollutants into the southern Baltic proper. Biological matrix-dependent variations found in the compositional pattern of chloronaphthalene congeners indicate selective and structure-dependent metabolism as well as the retention of some PCNs within a pelagic food chain studied.