For the examination of the irrigating stability of an environmentally-friendly construction method, the physical characteristics of living and natural materials, the irrigating and water scientific characteristics of streams, and the correlations among those characteristics and similar characteristics should be analyzed, and prior to this, sufficient database should be constructed for a long time. However, Korea is lack of those database and only the restricted database through sample sections are being used so it is quite much difficult to evaluate the stability of an environmentally-friendly construction method in terms of irrigation, flood control, and prevention of disasters. This paper compared and analyzed water depth and the distribution of the velocity of moving fluid through the numerical interpretation based on the changes in the arrangement of a water purification system. And then, it examined the characteristics of three-dimensional flow of a waterway. Through the test of an irrigation model, it installed a water purification system on a waterway in question and researched the irrigation stability of the waterway.