Abstract 1) We describe the hierarchical interplay of hydrology, hyporheic ecology and transformation of nutrients and pollutants in the hyporheic zone (HZ). The exchange of water between the surface-subsurface generates the hyporheic exchange flow: the engine that drives the ecological functioning of the HZ. The magnitude and direction of hydrological fluxes in the HZ follow complex spatial patterns, strongly influenced by the temporal dynamics of surface flow in rivers. 2) The direction and magnitude of hydrological fluxes also shapes the structure of hyporheic communities (hyporheos). During surface disturbances such as flooding or drought, benthic organisms may also use the HZ as a refuge, although the importance of this role is debated. 3) Streambed organisms differ in their ability to colonize the HZ depending on the biological traits they possess. The reduction in oxygen concentration and pore size with increasing sediment depth imposes a limit on the distribution of macroinvertebrates, which are replaced by a suite of smaller organisms (meiofauna and protists) at deeper sediment layers. Therefore, a concomitant reduction in net biomass and productivity might be expected through depth. However, only a few studies have assessed the contribution of the hyporheos to whole system production, and they have focused only on the fraction of relatively large organisms. 4) The bioreactor ability of the HZ to transform nutrients and pollutants is an important ecosystem service sustained by the life activities of hyporheos. Biofilms have the key role in this process due to their capacity to metabolize a wide range of dissolved compounds, including emerging pollutants. However, the residence time of water in pore sediments (resulting from hyporheic exchange flow) and the rest of the community (constantly reworking the sediments and grazing biofilms) are indirectly involved.