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How does the physical and chemical structure of the Critical Zone (CZ), defined as the zone from treetops to the bottom of groundwater, govern its hydro-biogeochemical functioning? Multiple lines of evidence from past and newly emerging research have prompted the shallow and deep partitioning concentration-discharge (C-Q) hypothesis. The hypothesis states that in-stream C-Q relationships are shaped by distinct source waters from flow paths at different depths. Base flows are often dominated by deep groundwater and mostly reflect groundwater chemistry, whereas high flows are often dominated by shallow soil water and thus mostly reflect soil water chemistry. The contrasts between shallow soil water versus deeper groundwater chemistry shape stream solute export patterns. In this context, the vertical connectivity that regulates the shallow and deep flow partitioning is essential in determining chemical contrasts, biogeochemical reaction rates in soils and parent rocks, and ultimately solute export patterns. This talk will highlight insights gleaned from multiple lines of recent studies that include collation of water chemistry data from soils, rocks, and streams in intensively monitored watersheds, meta-analysis of stream chemistry data at the continental scale, and integrated reactive transport modeling at the hillslope and watershed scales. The hypothesis underscores the importance of subsurface vertical structure and connectivity relative to the extensively studied horizontal connectivity. It also alludes to the potential of using streams as mirrors for subsurface water chemistry, and the potential of using C-Q relationships to infer flow paths and biogeochemical reaction rates and the response of earth’s subsurface to climate and human perturbations. Broadly, this simple conceptual framework links CZ subsurface structure to its functioning under diverse climate, geology, and land cover conditions.