The influence of an aqueous extract of diesel fuel was tested on growth of the marine eustigmatophyte Nannochloropsis (Monallantus) salina Hibberd. An increase in the concentration of the pollutant led to a decrease in growth rate as measured by optical density, with maximum effect observed (33% of control) at 100% aqueous pollutant. Spectrophotometric examination of cell viability (using Evan's blue dye) showed a significant negative effect of the diesel extract ( p ≤ 0.05, r = −0.92). Infrared spectra showed a slight change in the absorbance of contaminated compared with controlled cells. Proteome analysis (sodium dodecyl sulfate polyacrylamide gel electrophoresis -"SDS-PAGE") indicated that cell protein profiles depended on the pollutant concentration. Some of the resultant bands were characteristic to the pollutant concentration applied, indicating a distinct effect of the pollutant on the proteome structure. Iodine and toluidine blue dyes were applied using light microscopy to detect starch and mucilage, respectively. This indicated the presence of starch during all treatments, while the mucilage has been reduced. Transmission electron microscopy showed alterations to cell walls and membranes with different degrees of plasmolysis leading to a gradual increase in cell volume. However, the nucleus, the nucleolus and the pyrenoid remained unaffected. Similar results were obtained when the alga was cultured for 25 days in the 100% aqueous diesel extract indicating that long-term culture does not affect the degree of pollutant stress. Further, these cells recovered their normal appearance and characteristics within two days of being transferred to culture medium free of extract, indicating that N. salina shows a high tolerance to aqueous diesel fuel pollution.