Abstract: A method and system for modeling water flow quantity, quality, and fish biogenetics of a watershed restoration project. The modeling system allows a user to create a graphical representation of the different areas of a development site design. The graphical representation shows the water flows (quantity and quality) between the different areas. The user may also specify the attributes of each area, such as rate of infiltration, runoff coefficient, size, rate of evapotranspiration, and so on. The modeling system can simulate the impact of rainfall on the development design. The simulation determines the inflow (quantity and quality) of water to each area and determines the outflow (quantity and quality) of water for each area. The results of this simulation can be used to evaluate the development design and adjust the design to achieve the desired cost-benefit balance of the watershed protection criteria of choice.