Profile conditions were examined in both small experimental and pilot scale sub-surface flow wetlands. The study systems differed in their hydraulic design. The experimental systems had a vertical up-flow design whereas the pilot system was a horizontal flow trench design. Both systems were found to have significant physical, chemical and biological gradients within the sub-surface profile. System age and plant root density appear to be important factors in determining profile differentiation within the experimental systems. Root densities were found to be partitioned between the upper and lower layers on a 70%/30% split respectively. However, in the experimental systems as the systems aged and root densities increased beyond 112-251 g.m(-2) chemical water quality differentiation id the profile disappeared. Pilot scale systems were found to have physical gradients within the profile as evidenced by hydraulic short-circuiting. Vertical root density distribution is proposed as a major cause of this condition in horizontal flow systems.