Biofilm development in wastewater treatment system by soil infiltration is often mentioned for its participation to purification efficiency and clogging zone formation. It appears necessary to understand its evolution in order to better control the operation of these systems. The objective of this study was to improve knowledge about the temporal evolution of the biofilm structure in the first centimetres of infiltration system. For this purpose, metabolic fingerprints by Biolog EcoPlate (TM) and molecular fingerprints by Ribosomal Intergenic Spacer Analysis (RISA) were carried out on sand, septic effluent and treated effluent samples from two experimental reactors supplied with different hydraulic loads collected at different times. The metabolic capabilities of sand microflora decreased in time. In the same way, molecular structure of the biofilm community changed and converged to similar structure in time. Principal components analysis on RISA gel revealed a ''buffering effect'' of the sand filter on the genetic structure of the bacterial community from treated effluent. The kinetics of evolution of the both metabolic and genetic fingerprints showed a reduction of the metabolic and genetic potentials of septic and treated effluents for the same times. The population dynamic within the biofilms appears interesting evidence in the comprehension of the operation of the treatment systems.