Aims:The aims of this work were 1) To evaluate the performance of a submerged biofiltration system for the treatment of a surfactant-enriched wastewater that had been generated by a soil washing process. 2) To evaluate the effect of the flux and organic load over the performance of the system. 3) To determine the microbial evolution as an effect of the flux at different lengths of the biofilter by using a denaturing gradient gel electrophoresis (DGGE) analysis. Study Design: A three factorial design was used to evaluate the effect of different fluxes and organic loads over the performance of a continuously operated submerged aerobic biofilter. The DGGE technique was employed to determine microbial changes in the biofilter.