Abstract <p>Methods for the determination of polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and phthalic acid diesters (phthalates) in surface waters at trace concentration levels are considered. Lake Baikal, whose waters are characterized by trace levels of pollutants, was selected as a natural model for the study. The methods are combined into an analytical procedure including the collection of 1-L water samples, liquid–liquid extraction with <i>n</i>-hexane, preconcentration of the extracts, and analysis by gas chromatography–mass spectrometry. The accuracy indicator (±δ) for the determination of PCBs at concentrations from 0.02 to 0.90 ng/L ranges from 10 to 35%; for PAHs at concentrations from 0.10 to 15 ng/L, from 8.0 to 35%; and for phthalates at concentrations from 0.01 to 0.66 μg/L, from 12 to 38%. An online method for the determination of dominant phthalates in water by high-performance liquid chromatography has been validated, which reduces the risk of contamination of samples by background phthalates: sample volume 4 mL, concentration range 0.14–6.0 μg/L, and determination error 15–20%.</p>