Until now, water quality monitoring has relied heavily on spot sampling followed by instrumental analytical measurements to determine pollutant concentrations. Despite a number of advantages, this procedure has considerable limitations in terms of (i) temporal and spatial resolution that may be achieved at reasonable cost, and (ii) the information on bioavailability that may be obtained. Successful implementation of the Water Framework Directive (2000/60/EC) across EU member states will require the establishment and use of emerging and low-cost tools as part of monitoring programmes. These techniques may complement monitoring already in place by providing additional information with the aim to obtain a more representative picture of the quality of a water body. This article considers the limitations associated with current monitoring practice and presents, in the form of a review, emerging biological and chemical monitoring tools that may become part of a ‘toolbox’ of techniques for use by those in charge of assessing water quality. Biological monitoring techniques include biomarkers, biosensors, biological early warning systems and whole-organism bioassays. Sampling and analytical tools developed for chemical assessment comprise biosensors, immunoassays, passive samplers, and sensors. Descriptions of these devices and a discussion of their suitability for different types of monitoring detailing advantages and limitations are presented. Finally, quality assurance and quality control or method validation issues are summarised.