Our goal is to demonstrate the need to design a new type of environmentally friendly intrumentation to face the challenges of the Water Framework Directive. Rivers are spatially and timely structured ecological systems exhibiting hot spots and hot moments that contribute to their overall health status. However, current programs for monitoring water quality (grab samples and laboratory analysis) are based on sampling strategy that do not take into account the spatial and temporal heterogeneity of a water body. To reflect their actual dynamics, a paradigm shift is essential. This requires the development of new monitoring strategies and therefore new instrumentation. This new instrumentation must be able to measure at time scales appropriate to phenomena monitored and at a cost low enough to allow a sufficiently dense deployment in water bodies. We propose to enhance developing wireless networks of autonomous micro-sensors associated with mathematical processing of the collected data. The distinctive feature of this kind of smart sensor comes from the complete monitoring network expected, associating surface- and ground- waters chemistry, electronics and energy harvesting with smart data processing aiming to represent dynamic of basic ecological functions.