In recent decades the United Nations published that the scarcity of fresh water available for consumption could be a barrier to development of all countries. This reality becomes even more alarming considering the increased in population density, especially in megacities where water resources are still suffering because of punctual pollution sources. In underdeveloped countries this scenario is even more critical. Lack of financial resources for sanitation planning and implementation causes faster degradation of water bodies, bringing an imminent risk to these region populationsdue todisease spread, for example. In this way, its necessaryto reformulate the water resources monitoring projects, especially those placed in urban areas, used for large metropolitan areas supply, such as the Billings-Guarapiranga Complex, located in São Paulo. In these regions, rivers and reservoirs end up losing the characteristic of public assets and become abiotic elements in the landscape without cultural value or as a basic need for life. However, unfortunately the Brazilian current public management system is in crisis and so onweneed to innovate the way the monitoring projects is performed in order to reduce field work costs to collect samples and analyze them. In this context, the use of GIS tools, combined with the products obtained by remote sensors can effectively contribute to the reverse the current level freshwater ecosystems degradation. The idea is to create processes not only to assess the reservoirs quality, but also helpsto create and update the current master plans and ecological-economic zoning. This paper presents a set of tools to assist the water resources management, both in assessing of reservoirs trophic status, as in the analysis of catchment basin border ecological risk. It is possible to have a very concrete idea of the ecological risk associated with water resources through the phytoplankton biomass modeling by concentration of chlorophyll-A, the extraction of drainage networks and the analysis of land use in the catchment basin can. The results obtained here compared to others, points out the potential of the proposed methodologies. Furthermore, processing of Landsat 5/TM series helped in identifying chlorophyll-A concentration spatial dynamics, allowing the identification persistent contamination areas in 2003 and 2010. Finally, we believed the reader should feel encouraged to develop new models and update the current ones. The set of proposed tools can effectively contribute to the water resourcesmanagement.