A landfill leachate collection system (LCS) is intended to collect and remove leachate for treatment, thereby reducing the driving force (hydraulic head) for advective contaminant transport through the liner system. However the long-term performance of the granular drainage layer and pipes conducting the leachate to the sump(s) for collection is greatly affected by the leachate characteristics. A calibrated numerical model ‘BioClog’ is used to examine the differences between the chemical characteristics of the leachate between when it first enters and after it has passed through a granular drainage layer. The results show that the treatment of leachate within the filter layer and drainage layer can substantially reduce the leachate concentrations between its first entry into the system and its collection. This change in concentration is directly associated with the clogging of, and consequent leachate mounding within, the drainage layer. Thus the leachate collected at the sumps generally does not represent the leachate entering the LCSs and therefore should not be used directly as the source leachate concentrations for designing the LCSs when the clogging of systems needs to be addressed.