Cis-trans isomerization of unsaturated fatty acids is a crucial adaptive reaction of Pseudomonas and Vibrio species to toxic organic compounds or other environmental stress factors. In order to test the long-term performance of this adaptive mechanism as well as to assess its application as biomarker for environmental contamination studies were performed in batch cultures and in continuously running sand columns, simulating long-term contamination with bisphenol A (BPA). In short-term grown batch cultures a high correlation between trans/cis ratio and added BPA concentration and toxicity was observed. In contrary, this did not occur in the case of long-term sand columns. An increase in trans/cis ratio of unsaturated fatty acids only appeared in a limited period of time. Afterwards the trans/cis ratio reached the values measured for non-stressed cultures. Cis-trans isomerization is only an urgent response mechanism that is later substituted by other adaptive mechanisms. Therefore, it can be concluded that the trans/cis ratio of unsaturated fatty acids was shown not to be an appropriate biomarker for durable stress in the environment.