A bacterial model system (Pseudomonas putida DSM 50026) was used in this research to assess toxicity of the environmentally relevant concentrations of mercury species (MeHg and Hg(II)) that represent important pollutants of aquatic ecosystems at sites of industrial or mining activities. In addition to direct monitoring of bacterial growth, we also analyzed fatty acid profiles of exposed and non-exposed cultures to determine possible toxic effects manifested on membrane level. The results showed that exposure of P. putida to Hg(II) in concentrations of 0.2–200 µg/L did not have any significant effects on growth nor fatty acid composition of exposed bacterial culture. On the other hand, when bacteria were exposed to up to 1600-times lower concentrations of MeHg (0.12–12.5 µg/L), growth inhibition as well as significant changes in fatty acid composition were detected. Observed adaptive membrane changes due to MeHg exposure were similar to those associated with responses to organic solvents and some other membrane-disrupting compounds.