The monitoring or water quality usually involves spot or bottle sampling followed by instrumental analysis to determine pollutant concentrations. Despite many advantages, this method bas limitations in terms of temporal and spatial resolution that may be achieved at reasonable cost, and in the bioavailability assessment or pollutants. The successful implementation or the Water Framework Directive (2000/60/EC) across EU member-states will require the establishment and use or alternative emerging and low-cost tools as part or water quality monitoring programmes in the future. These techniques may complement monitoring already in place by providing additional information with the aim of obtaining a more representative picture or the status or a water body. This article discusses the requirements or the Water Framework Directive and outlines a number of biological and chemical monitoring methods or tools that could be used in the future to support and underpin the Directive.