Watershed analysis is a method used to collectively characterize ecosystem elements present within a watershed. Wastewater flow and pollutant content help to define the appropriate wastewater treatment system necessary to treat the wastewater within the watershed. Watershed monitoring aids to investigate the potential contamination through analysis of surface waterbodies. Major contamination sources can be broadly classified as non-point and point sources of pollution, with contaminants of concern like nitrogen, phosphorous, coliforms, organic compounds and turbidity. The wastewater distribution, contaminant loadings and annualized treatment costs to the Siuslaw Watershed on the central Oregon coast were estimated from both the centralized system and the decentralized systems in the watershed. Additionally an extensive performance analysis of newer technologies and improvements to the existing systems in the form of advanced treatments was done to assess their feasibility. An analysis of contaminant loading from septic to the Oak Creek Watershed, located about 50 miles inland near Corvallis, Oregon, was conducted for nitrate, nitrite, ammonia and ortho-phosphate. The basic objective was to evaluate impact of regions with septic systems within the two watersheds. Computer based ArcGIS model can be developed to understand the response of flows and contaminants to a watershed. The studies presented in this dissertation provides the basis for predicting estimates of wastewater flow from residential and non-residential catchments and addresses data gaps for determining fate and transport of contaminants within the watershed based on land use. In addition spreadsheet interface was developed for the analysis of centralized and decentralized zones.