Background Surface water quality has been deteriorating in recent decades, due to the emission of chemical compounds (e.g. heavy metals, pesticides, nutrients and fertilisers), physical alterations (e.g. infrastructure, dams and fixed water levels) and the presence of harmful organisms such as cyanobacteria. Due to climate change, the latter is becoming an increasing serious health risk and is causing significant economic damage. The Water Framework Directive (WFD) sets out to improve the chemical and ecological quality of European surface waters by the end of 2015. Since no absolute standards can be set, due to the great ecological variety of surface water across the EU, national metric standards have been developed for a number of ecological quality parameters. Two of these parameters for ecological quality are the presence of and the species variety within phytobenthos (microscopic plant life on the bottom of the surface water) and phytoplankton (microscopic plant life in the surface water). Both are highly dependent on the chemical quality and the eutrophication status of the surface water, but they are hard to quantify. The composition of the phytobenthos and phytoplankton is currently measured by analysing water samples underneath a microscope and visually determining the presence and quantity of the species present in the sample. This technique is very laborious, time consuming, prone to errors and bias, and is not absolutely quantitative. As a result, these ecological parameters, though prevailing over chemical parameters, are only measured on a very limited basis, preventing rapid detection and subsequent action against changes in water quality. Objectives The Hydrochip project aims to demonstrate a new measuring device called Hydrochip, which will provide an opportunity to monitor the implementation of the WFD with regard to the ecological parameters phytobenthos and phytoplankton in an innovative way. The main objectives of the project are to: Demonstrate that Hydrochip can be used to reliably, quantitatively and efficiently determine ecological water quality in a high throughput fashion by using molecular biomarkers to determine phytobenthos (diatoms) and phytoplankton (cyanobacteria). Demonstrate that Hydrochip is a good alternative to the standard techniques currently employed to determine phytobenthos and phytoplankton in surface water samples. Demonstrate and validate that Hydrochip can be easily adapted to determine ecological quality parameters in other European surface waters with a different ecological make up. Disseminate the project results to target groups using a comprehensive networking approach. Contribute to the integration of the results in European water policies. Expected results: Demonstration of Hydrochip’s reliable use in determining ecological water quality parameters in The Netherlands to the same or to a wider extent than the standard method and in a cost-effective way. The results will be shown to be readily adaptable to other European surface waters that have different ecological make ups and are able to contribute to new national and European policies on metric standards for ecological water quality parameters.