We investigated the coupling of abundance of bacteria, phytoplankton and ciliates with hydrocarbons in the surface water and sediments of five interconnected ponds in the arid Sfax solar salterns. This study aimed at determining the potential sources of hydrocarbons and the effects of salinity gradients on microorganism metabolism. Hydrocarbon analysis was performed by gas chromatography (GC-FID) and gas chromatography coupled with mass spectrometry (GC-MS). The GC-FID allowed the detection of aliphatic hydrocarbons and n-alkanes ranging from n-C13 to n-C30. Total aliphatic hydrocarbon concentrations varied from 92.5 mg. l−1 in the first pond (having marine characteristics) to 661.1 mg. l−1 in the last pond (crystallizer) (316.8±120.1 mg. l−1) for water samples and from 26.7 to 127.8 !g. g−1 dry weight for sediment samples. The GC-MS enabled us to detect halogenated hydrocarbons (bromoalkanes and chloroalkanes) and n-alkenes. The distribution of n-alkanes indices coupled to several environmental factors suggests that a major fraction of hydrocarbons resulted from both prokaryotic (bacteria) and eukaryotic (protists) developments. A low hydrocarbon fraction might be petrogenic.