One of the main differences between landscape ecology and other branches of ecology is the application of spatial concepts in ecological planning. Compared to the classical planning approach based on economic land suitability, the principles of landscape ecology are helpful in conserving the ecological processes of landscapes and simultaneously their steady changes. The aim of this study is to propose the application of the principles of landscape ecology in improving the quality of urban rivers, which could help in defining sustainable landscape development. The Khoshk River, located in an arid and semi-arid climate, crosses the city of Shiraz. This river, as the case of this study, has been under pressure due to simplification of its complex natural pattern resulting from the growth of the city. The impact of unplanned development of housing, agriculture and industries have threatened Khoshk River’s natural environment. The research method is based on assessment of human and biophysical units. Zoning in different scales and determining the appropriate indicators based on the theoretical framework of the study and site characteristics help assess the ecological potentials and limitations. The results facilitate policy making and defining strategies for improving the Khoshk River ecological system. The method for analyzing the quality of urban rivers may be generalized in similar situations.