Integrated river management is based on monitoring, modelling and assessment of the water cycle. Effective and efficient management is only possible when these three activities are well interconnected and concerted. The choice of appropriate, high quality monitoring techniques is probably one of the most crucial factors in the assessment of river systems. To this end, the EU has recently adopted a Water Framework Directive. Although this Directive provides the guidelines for monitoring water bodies, local governments still have a lot of freedom regarding their practical implementation. The development of a consistent monitoring and assessment strategy and methodology is therefore essential for each European country. This paper discusses different Flemish techniques for the monitoring and assessment of macro-invertebrates and fish communities in relation to water quantity and the physical, chemical, morphological and structural quality. Finally, a concept for sustainable and integrated ecological assessment and management is presented.