The World Resources Institute reported that nearly half of the world population will experience water shortage in 2030; the effects of floods will be tripled globally. Drought and floods threaten several cities all around the country, including Istanbul. The most important factors that control the physical environment are stream systems and their basins. Are the stream basin systems ready for this process? Hydraulic system balanced in its natural basin has lost its natural morphology and direction of overland flowing because of land decisions given wrongly by the authorities. This situation shows that it is essential to analyze the physical structure of stream/river ecosystems and land use decisions on the urban, national, and international scales. The lack of integrated water law, management problems, and the laws against the protection of stream systems have caused the problem. The present study focuses on the 3344 km long stream systems that are in the basins of 168 running streams and in nearly 2740 km2 outside drinking water basin in Istanbul. The findings show that 73% of the stream systems have protected their natural structure, 27% have transformed its natural structure, and 79% have protected their natural structure in rural areas according to longitude. Of the stream systems, 21% have transformed its natural structure in urban areas because of various interventions, but they have not disappeared, they have been affected by land use decisions, and stream protective zones have been deforced. Based on the stream basin scale, 64% of the region have been affected because of the transformation, and some environmental risk, such as floods and drought, have been spread to the whole city. The findings show that streams are not independent from each other; laws must evaluate streams on the basin system scale, and streams are important internationally as they are open basin systems. Integrated basin planning and management, sustainable stream restoration program, and holistic water law controlled by the government are essential to find solutions to legal, technical, and corporate problems; protect natural stream systems; maintain their sustainability; and overcome the risks.