Studies of links between hyporheic exchange processes and benthic ecology have been constrained by the practical difficulties inherent in coupling accurate measurements of small-scale flows of water in and out of streambeds with the collection of quantitative biological samples. For the first time we present details of a new experimental facility in Dorset, England to artificially generate replicated up and downwelling zones in a natural streambed. We detail its design, construction and calibration with natural vertical hydraulic exchange magnitudes as well as setting out the research questions that this facility will be used to address. These include definitive studies of the links between vertical hydraulic exchange and macroinvertebrate, meiofaunal, phytobenthic and macrophyte communities, investigation of cause and effect relationships between water chemistry parameters and the biota, and studies of how hyporheic residence times affect chemical transformations and microbial processes. Becoming operational in summer 2007, this new facility offers the potential for new studies on links between stream ecology and hyporheic processes.