Triton X-100, as one of the most popular surfactants used in bioremediation techniques, has been reported as an effective agent enhancing the biodegradation of hydrocarbons. However efficient, the surfactant’s role in different processes that together enable the satisfying biodegradation should be thoroughly analysed and verified. In this research, we present the interactions of Triton X-100 with the bacterial surfaces (hydrophobicity and zeta potential), its influence on the enzymatic properties (considering mono- and dioxygenases) and profiles of fatty acids, which then all together were compared with the biodegradation rates. The addition of various concentrations of Triton X-100 to diesel oil system revealed different cell surface hydrophobicity (CSH) of the tested strains. The results demonstrated that for Pseudomonas stutzeri strain 9, higher diesel oil biodegradation was correlated with hydrophilic properties of the tested strain and lower Triton X-100 biodegradation. Furthermore, an increase of the branched fatty acids was observed for this strain.Electronic supplementary materialThe online version of this article (doi:10.1007/s11356-014-3668-z) contains supplementary material, which is available to authorized users.