The aim of this research was to use experimental planning to collect data and also to establish a methodology to compare them with theoretical data, where both are associated to the dynamics of reduction in pollutants in a natural treatment system for wastewater. The experimental data were collected and evaluated from two of these systems, built according to Valentim & Amendola (1999) and Collaço (2001), at the Center of Mechanization and Agricultural Automation of the Agricultural Institute of Campinas, located in Jundiaí, SP, Brazil. These systems were rectangular in shape; one with crushed stone and another with chopped tires used as support bed to hold the plants, both with macrophyte species Typha sp. The theoretical data were obtained from a mathematical model, adapted to describe the physical process of subsurface flow. The numerical simulations using the implicit finite difference numerical method were carried out using MATLAB 6.1 software. The results of the comparative analysis between theoretical and experimental data are presented for the two types of support beds. Some coefficients and parameters were adjusted to characterize the constructed systems. The results obtained were analyzed and some conclusions about the physical process as well as those about the adequacy of the mathematical model were made.