Sustainable carbon fixation system with large scale afforestation in arid land has been proposed for the mitigation of global warming. To avoid the problem of rainfall shortage and the large evaporation loss, our afforestation system has adopted a water-harvesting system. We have set a research site near Leonora (mean annual rainfall and evaporation are about 200 mm and 2,500 mm, respectively), Western Australia. We have so far developed an original runoff simulation model for understanding of water behavior involving penetration, evaporation and runoff. In previous studies, the best values of corrective coefficient of penetration (PR), and equivalent roughness coefficient (N) were determined by fitting numerical results to the water level data of the collecting pond of a watershed within 6 km × 4.8 km. In the present paper we extend this model to the larger area of 43 km × 52 km to evaluate the change in water penetration before and after the afforestation of bare ground, assuming that penetration rate of the bare ground changes to that of woodland by the afforestation. Then we evaluate effect of afforestation on penetration water amount by comparing the calculated results before and after afforestation in the large area. Finally we show the strategy to select appropriate afforestation sites and the way to evaluate the effects of afforestation on the vegetation of the peripheral areas.