This study investigated the physicochemical interactions between a rhamnolipid biosurfactant and a biofilm layer. A concentration of 300 μg mL(-1) of rhamnolipids, which is around the critical micelle concentration value (240 μg mL(-1)), showed great potential for reducing biofilm. The surface free energy between the rhamnolipids and biofilm layer decreased, as did the negative surface charge, due to the removal of negatively charged humic-like, protein-like, and fulvic acid-like substances. The carbohydrate and protein concentrations composed of extracellular polymeric substances decreased by 31.6% and 79.6%, respectively, at a rhamnolipid concentration of 300 μg mL(-1). In particular, rhamnolipids can interact with proteins, leading to a reduction of the N source and amide groups on the membrane. For carbohydrates, the component ratio of glucosamine was decreased, but the levels of glucose and mannose that form the majority of the carbohydrates remained unchanged. To our knowledge, the present study is the first attempt at studying the interactions of the two phases of rhamnolipids and the biofilm layer, and as such is expected to clarify the mechanism by which rhamnolipids lead to a reduction in biofilm.