The quantification of 14 polycyclic aromatic hydrocarbons (PAHs) was carried out in sediment samples collected from Akaki River, Lake Awassa, and Lake Ziway, Ethiopia. The concentration of PAHs in the samples was determined using gas chromatography-mass spectrometry (GC-MS) in selected ion monitoring (SIM) mode, after microwave-assisted extraction (MAE), using acetone/n-hexane (1:1, v/v) mixture. The accuracy of the method was determined by extracting and analyzing New York/New Jersey waterway sediment standard reference material (SRM 1944). The measured concentrations of PAHs in SRM 1944 agreed well with the certified values. In samples from Akaki River, Lake Awassa, and Lake Ziway, the total content of PAHs determined ranged from 0 to 3070 ng/g (average 534 ng/g), 24.9 to 413 ng/g (average 169 ng/g), and 15.0 to 305 ng/g (average 175 ng/g), respectively. Source ratios indicated that the PAHs were mainly from petrogenic origin. Sediments from all sampling sites indicated negligible levels of toxicity with no risk of adverse biological effects.