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ABSTRACT The importance of subsurface water dynamics, such as water storage and flow partitioning, is well recognised. Yet, our understanding of their drivers and links to streamflow generation has remained elusive, especially in small headwater streams that are often data‐limited but crucial for downstream water quantity and quality. Large‐scale analyses have focused on streamflow characteristics across rivers with varying drainage areas, often overlooking the subsurface water dynamics that shape streamflow behaviour. Here we ask the question:What are the climate and landscape characteristics that regulate subsurface dynamic storage, flow path partitioning, and dynamics of streamflow generation in headwater streams?To answer this question, we used streamflow data and a widely‐used hydrological model (HBV) for 15 headwater catchments across the contiguous United States. Results show that climate characteristics such as aridity and precipitation phase (snow or rain) and land attributes such as topography and soil texture are key drivers of streamflow generation dynamics. In particular, steeper slopes generally promoted more streamflow, regardless of aridity. Streams in flat, rainy sites (< 30% precipitation as snow) with finer soils exhibited flashier regimes than those in snowy sites (> 30% precipitation as snow) or sites with coarse soils and deeper flow paths. In snowy sites, less weathered, thinner soils promoted shallower flow paths such that discharge was more sensitive to changes in storage, but snow dampened streamflow flashiness overall. Results here indicate that land characteristics such as steepness and soil texture modify subsurface water storage and shallow and deep flow partitioning, ultimately regulating streamflow response to climate forcing. As climate change increases uncertainty in water availability, understanding the interacting climate and landscape features that regulate streamflow will be essential to predict hydrological shifts in headwater catchments and improve water resources management. 

Woody encroachment is a widespread phenomenon in grassland ecosystems, driven by overgrazing, fire suppression, nitrogen deposition and climate change, among other environmental changes. The influence of woody encroachment on processes such as chemical weathering however is poorly understood. In particular, for fast reactions such as carbonate weathering, root traits associated with woody encroachment (e.g., coarser, deeper, and longer residence times) can potentially change fluxes of inorganic carbon into streams and back to the atmosphere, providing CO2-climate feedbacks. Here we examine the influence of deepening roots arising from woody encroachment on catchment water balance and carbonate weathering rates at Konza a tallgrass prairie within a carbonate terrain where woody encroachment is suspected to drive the groundwater alkalinity upwards. We use a watershed reactive transport model BioRT-Flux-PIHM to understand the ramifications of deepening roots. Stream discharge and evapotranspiration (ET) measurements were used to calibrate the hydrology model. The subsurface CO2 concentration, water quality data for groundwater, stream, soil water and precipitation were used to constrain the soil respiration and carbonate dissolution reaction rates. The hydrology model has a Nash-Sutcliffe Efficiency value of 0.88. Modelling results from numerical experiments indicate that woody encroachment results in overall lower stream flow due to higher ET, yet the groundwater recharge is higher due to deep macropore development from deepening roots. The deeper macropores enhance carbonate weathering rate as more acidic, CO2-rich water recharges the deeper calcite bedrock. Accounting for the change in inorganic carbon fluxes caused by such land use changes gives a better estimate of carbon fluxes in the biosphere. Such knowledge is essential for effective planning of climate change mitigation strategies. 

Abstract. Watersheds are the fundamental Earth surface functioning units that connect the land to aquatic systems. Many watershed-scale models represent hydrological processes but not biogeochemical reactive transport processes. This has limited our capability to understand and predict solute export, water chemistry and quality, and Earth system response to changing climate and anthropogenic conditions. Here we present a recently developed BioRT-Flux-PIHM (BioRT hereafter) v1.0, a watershed-scale biogeochemical reactive transport model. The model augments the previously developed RT-Flux-PIHM that integrates land-surface interactions, surface hydrology, and abiotic geochemical reactions. It enables the simulation of (1) shallow and deep-water partitioning to represent surface runoff, shallow soil water, and deeper groundwater and of (2) biotic processes including plant uptake, soil respiration, and nutrient transformation. The reactive transport part of the code has been verified against the widely used reactive transport code CrunchTope. BioRT-Flux-PIHM v1.0 has recently been applied in multiple watersheds under diverse climate, vegetation, and geological conditions. This paper briefly introduces the governing equations and model structure with a focus on new aspects of the model. It also showcases one hydrology example that simulates shallow and deep-water interactions and two biogeochemical examples relevant to nitrate and dissolved organic carbon (DOC). These examples are illustrated in two simulation modes of complexity. One is the spatially lumped mode (i.e., two land cells connected by one river segment) that focuses on processes and average behavior of a watershed. Another is the spatially distributed mode (i.e., hundreds of cells) that includes details of topography, land cover, and soil properties. Whereas the spatially lumped mode represents averaged properties and processes and temporal variations, the spatially distributed mode can be used to understand the impacts of spatial structure and identify hot spots of biogeochemical reactions. The model can be used to mechanistically understand coupled hydrological and biogeochemical processes under gradients of climate, vegetation, geology, and land use conditions. 

Abstract Reactive Transport Models (RTMs) are essential tools for understanding and predicting intertwined ecohydrological and biogeochemical processes on land and in rivers. While traditional RTMs have focused primarily on subsurface processes, recent watershed‐scale RTMs have integrated ecohydrological and biogeochemical interactions between surface and subsurface. These emergent, watershed‐scale RTMs are often spatially explicit and require extensive data, computational power, and computational expertise. There is however a pressing need to create parsimonious models that require minimal data and are accessible to scientists with limited computational background. To that end, we have developed BioRT‐HBV 1.0, a watershed‐scale, hydro‐biogeochemical RTM that builds upon the widely used, bucket‐type HBV model known for its simplicity and minimal data requirements. BioRT‐HBV uses the conceptual structure and hydrology output of HBV to simulate processes including advective solute transport and biogeochemical reactions that depend on reaction thermodynamics and kinetics. These reactions include, for example, chemical weathering, soil respiration, and nutrient transformation. The model uses time series of weather (air temperature, precipitation, and potential evapotranspiration) and initial biogeochemical conditions of subsurface water, soils, and rocks as input, and output times series of reaction rates and solute concentrations in subsurface waters and rivers. This paper presents the model structure and governing equations and demonstrates its utility with examples simulating carbon and nitrogen processes in a headwater catchment. As shown in the examples, BioRT‐HBV can be used to illuminate the dynamics of biogeochemical reactions in the invisible, arduous‐to‐measure subsurface, and their influence on the observed stream or river chemistry and solute export. With its parsimonious structure and easy‐to‐use graphical user interface, BioRT‐HBV can be a useful research tool for users without in‐depth computational training. It can additionally serve as an educational tool that promotes pollination of ideas across disciplines and foster a diverse, equal, and inclusive user community. 

Abstract Terrestrial production and export of dissolved organic and inorganic carbon (DOC and DIC) to streams depends on water flow and biogeochemical processes in and beneath soils. Yet, understanding of these processes in a rapidly changing climate is limited. Using the watershed‐scale reactive‐transport model BioRT‐HBV and stream data from a snow‐dominated catchment in the Rockies, we show deeper groundwater flow averaged about 20% of annual discharge, rising to ∼35% in drier years. DOC and DIC production and export peaked during snowmelt and wet years, driven more by hydrology than temperature. DOC was primarily produced in shallow soils (1.94 ± 1.45 gC/m²/year), stored via sorption, and flushed out during snowmelt. Some DOC was recharged to and further consumed in the deeper subsurface via respiration (−0.27 ± 0.02 gC/m²/year), therefore reducing concentrations in deeper groundwater and stream DOC concentrations at low discharge. Consequently, DOC was primarily exported from the shallow zone (1.62 ± 0.96 gC/m²/year, compared to 0.12 ± 0.02 gC/m²/year from the deeper zone). DIC was produced in both zones but at higher rates in shallow soils (1.34 ± 1.00 gC/m²/year) than in the deep subsurface (0.36 ± 0.02 gC/m²/year). Deep respiration elevated DIC concentrations in the deep zone and stream DIC concentrations at low discharge. In other words, deep respiration is responsible for the commonly‐observed increasing DOC concentrations (flushing) and decreasing DIC concentrations (dilution) with increasing discharge.  DIC export from the shallow zone was ~66% of annual export but can drop to ∼53% in drier years. Numerical experiments suggest lower carbon production and export in a warmer, drier future, and a higher proportion from deeper flow and respiration processes. These results underscore the often‐overlooked but growing importance of deeper processes in a warming climate. 

ABSTRACT Woody encroachment—the expansion of woody shrubs into grasslands—is a widely documented phenomenon with global significance for the water cycle. However, its effects on watershed hydrology, including streamflow and groundwater recharge, remain poorly understood. A key challenge is the limited understanding of how changes to root abundance, size and distribution across soil depths influence infiltration and preferential flow. We hypothesised that woody shrubs would increase and deepen coarse‐root abundance and effective soil porosity, thus promoting deeper soil water infiltration and increasing soil water flow velocities. To test this hypothesis, we conducted a study at the Konza Prairie Biological Station in Kansas, where roughleaf dogwood (Cornus drummondii) is the predominant woody shrub encroaching into native tallgrass prairie. We quantified the distribution of coarse and fine roots and leveraged soil moisture time series and electrical resistivity imaging to analyse soil water flow beneath shrubs and grasses. We observed a greater fraction of coarse roots beneath shrubs compared to grasses, which was concurrent with greater saturated hydraulic conductivity and effective porosity. Half‐hourly rainfall and soil moisture data show that the average soil water flow through macropores was 135% greater beneath shrubs than grasses at the deepest B horizon, consistent with greater saturated hydraulic conductivity. Soil‐moisture time series and electrical resistivity imaging also indicated that large rainfall events and greater antecedent wetness promoted more flow in the deeper layers beneath shrubs than beneath grasses. These findings suggest that woody encroachment alters soil hydrologic processes with cascading consequences for ecohydrological processes, including increased vertical connectivity and potential groundwater recharge.