In the last decade in particular, Serbia encountered the problems of drinking water supply, which influenced the perception of professional public about the water crisis but also started more intensive work on water resource perseverance as well as the implementation of European Water Directive. One of the main demands of the Directive focuses on integrated river basin management (IRBM), which is a complex and a large task. The need to collect data on water quality and quantity, specific and key issues of water management in Južna Morava river basin, pressures on river ecosystem, flood risks and erosion problems, cross-border issues, socioeconomic processes, agricultural development as well as protected areas, and also to give the measures for solving problems and pressures recognized in the basin, is undisputable. This paper focuses on detailed analysis of specific pressures on river ecosystem and composition of recommendations for integrated management of Južna Morava river basin as cross-border river basin, taking into the account European experiences in IRBM. [Projekat Ministarstva nauke Republike Srbije, br. 43007: Istraživanje klimatskih promena na životnu sredinu - praćenje uticaja, adaptacija i ublažavanje, podprojekat br. 9: Učestalost bujičnih poplava, degradacija zemljišta i voda kao posledica globalnih promena]