The results from the measurements of aliphatic hydrocarbons suggest that hydrocarbons in the Point Loma Wastewater Treatment Plant (PLWTP) effluents are mainly petroleum derived; those in the Tijuana River runoff have largely originated from terrestrial plants with visible petroleum contamination; and those in the sea surface microlayer, sediment traps, and sediments at various coastal locations off San Diego have mostly resulted from biogenic contributions with enhanced microbial products in the summer season. Rainfall in the winter season appeared to amplify the inputs from terrestrial higher plants to the coastal areas. The PLWTP discharged approximately 3.85 metric tons of n-alkanes (C 10 -C 35 ) in 1994, well below the level (136 metric tons) estimated in 1979. The input of aliphatic hydrocarbons from the Tijuana River was about 0.101 metric tons in 1994. Diffusion, solubilization, evaporation, and microbial degradation seemed partially responsible for the difference in the concentrations and compositions of aliphatic hydrocarbons in different sample media, although the relative importance of each mechanism cannot be readily discerned from the available data. The results from analyses of aliphatic hydrocarbon compositional indices are generally consistent with those of polycyclic aromatic hydrocarbons.