A computer program called Hydropower Plant Site Assessment Program (HPSAP) is developed by using Visual Basic Programming with visual application interface in Microsoft Excel to assess the hydropower potential in river basins.A searching algorithm methodology to select optimum site to install the Run-of-River hydropower plants is developed according to hydrological, metrological and economic criteria. HPSAP has several options to analyze the watershed for different head or power criteria. HPSAP has ten application forms to input the searching requirement criteria and eight outputs tables with one basin map to screen the locations of proposed plants. HPSAP estimates the locations coordinates and upstream drainage area for powerhouse and weir locations, elevation of powerhouse and weir, distance from weir to powerhouse, approximate penstock length, design head and generated power for each proposed Run-of-River hydropower plants. HPSAP uses a flow duration curve mathematical expression developed by Gene expression programming to estimate the design discharge for the plant based on rainfall runoff model outputs. HEC-HMS model is used as hydrological rainfall runoff model in this study.