Surface sediment samples from Al-Qahma lagoon in the southern part and Al-Wajh lagoon in the northern part of the Red Sea coast of Saudi Arabia were collected by a Van Veen grab sampler to determine the characteristics, distribution, and sources of aliphatic and cyclic hydrocarbons. The total extractable organic matter (TEOM) was extracted with a dichloromethane/methanol mixture after drying and sieving the sediments and identified by gas chromatography–mass spectrometry. The TEOM comprised n-alkanes (302.6 ± 446.7 ng·g−1 and 64 ± 50 ng·g−1), hopanes (29.8 ± 132.3 ng·g−1 and 1.0 ± 2.5 ng·g−1), steranes (0.0 and traces), n-alkanoic acids (745.8 ± 799.6 ng·g−1 and 120.7 ± 92.0 ng·g−1), n-alkanols (457.4 ± 1085.6 ng·g−1 and 49.7 ± 32.3 ng·g−1), polycyclic aromatic hydrocarbons (PAHs) (54.5 ± 96.8 ng·g−1 and 7.8 ± 8.5 ng·g−1), and phthalates (185.3 ± 169.9 ng·g−1 and 67.4 ± 70.4 ng·g−1) in the Al-Qahma and Al-Wajh lagoon sediments, respectively. The percentages of the various sources relative to total aliphatic and cyclic hydrocarbon concentrations were 6.9 ± 6% for terrestrial plants, 53.7 ± 19% for algae, 10 ± 2% for microbial, 16 ± 12% for petroleum, and 13.4 ± 7 for plasticizer inputs in Al-Qahma lagoon. In Al-Wajh lagoon, they were 9.7 ± 4% for terrestrial plants, 30.8 ± 14% for algae, 25.2 ± 5% for bacteria, 11.2 ± 3% for petroleum, and 23.1 ± 11% for plasticizers.