Recently, the population growth and agricultural development are rapidly undergoing in the South-West Texas. The junction of three river basins such as Lavaca river basin, Colorado-Lavaca Coastal basin and Lavaca-Guadalupe Coastal basin, are interesting for non-point and point source pollutant modeling: Especially, the 2 basins are an intensively agricultural region (Colorado-Lavaca Coastal/Lavaca-Guadalupe Coastal basins) and several cities are rapidly extended. In case of the Lavaca river basin, there are many range land. Several habitat types wide-spread over three relatively larger basins and five wastewater discharge regions are located in there. There are different hazardous substances which have been released. Total nutrient loads are composed of land surface load and river load as Non-point source and discharge from wastewater facilities as point source. In 3 basins region, where point and non-point sources of poll Jtion may be a big concern, because increasing fertilizers and pesticides use and population cause. This project objective seeks to how to assess and control the accumulation of non-point and point source and discuss the main impacts of agriculture and environmental concern as non-point source with water quality related to pesticides, fertilizer, and nutrients and as point source with wasterwater discharge from cities. The GIS technique has been developed to aid in the point and non-point source analysis of impacts to natural resource within watershed. This project shows the losses in $kg/km^2/year$ of BOD (Biological Oxygen Demand), TN (Total Nitrogen) and TP (Total Phosphorus) in the runoff from the surface of 3 basins. In the next paper, sediment contamination will show how to evaluate in Estuarine habitats of these downstream.