Changes in land use/management can have profound effects on the amounts, speciation, and timing of nutrient and water exports to coastal systems. Therefore, management and policy focused on water quantity and quality issues in lakes and the coastal ocean need to be informed by research on the hydrological and biogeochemical linkages within watersheds and between watershed and the receiving water body. However, our mechanistic understanding of the nature of these linkages across different spatial and temporal scales is still limited. Hence, much remains to be done to develop simulation models that adequately represent hydrological and biogeochemical processes, and their coupling, along the aquatic continuum. We invite observational, theoretical, and modeling contributions on 1) the scale dependencies of water flows and biogeochemical linkages between terrestrial, river and lacustrine/coastal ecosystems, 2) the effects of climatic, land-use and anthropogenic forcings on hydrological and biogeochemical processes across scales, and 3) the time-dependent and coupled watershed state variables that are critical to understand ecosystem impacts in the receiving water bodies.