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Transient storage zones for water represent potential hot spots for metabolic activity in streams. In lowland rivers, the high abundance of submerged vegetation can increase water transient storage, bioreactive surface areas, and, ultimately, in‐stream metabolic activity. Changes in flow resulting from climatic and anthropogenic factors that influence the presence of aquatic vegetation can also, thereby, impact in‐stream metabolism and nutrient cycling. We investigated the effects of water column depth on aquatic vegetation cover and its implications on water transient storage and associated metabolic activity in stream mesocosms (n= 8) that represent typical conditions of lowland streams. Continuous injections of metabolically reactive (resazurin‐resorufin) tracers were conducted and used to quantify hydraulic transport and whole‐mesocosm aerobic respiration. Acetate, a labile carbon source, was added during a second stage of the tracer injection to investigate metabolic responses. We observed both higher vegetation coverage and resazurin uptake velocity, used as a proxy of mesocosm respiration, with increasing water column depth. The acetate injection had a slight, positive effect on metabolic activity. A hydrodynamic model estimated the water transport and retention characteristics and first‐order reactivity for three mesocosms. These results suggest that both the vegetated surface water and sediments contribute to metabolically active transient storage within the mesocosms, with vegetation having a greater influence on ecosystem respiration. Our findings suggest that climate and external factors that affect flow and submerged vegetation of lowland rivers will result in changes in stream respiration dynamics and that submerged vegetation is a particularly important and sensitive location for stream respiration. Ecosystem respiration is positively correlated with water depth, discharge, and vegetation coverageIn‐stream vegetation beds are significant sites of metabolically active transient storageDeclining stream flows may negatively impact aquatic vegetation and ecosystem function in lowland rivers

Anomalous transport cannot be adequately described with classical Fickian advection‐dispersion equations (ADE) with constant coefficients. Rather, fractional calculus models may be used, which capture salient features of anomalous transport (e.g., skewness and power law tails). FracFitis a parameter estimation tool based on space‐fractional and time‐fractional models used by the hydrology community. Currently, four fractional models are supported: (1) space‐fractional advection‐dispersion equation (sFADE), (2) time‐fractional dispersion equation with drift (TFDE), (3) fractional mobile‐immobile (FMIM) equation, and (4) temporally tempered Lévy motion (TTLM). Model solutions using pulse initial conditions and continuous injections are evaluated using stable distributions or subordination integrals. Parameter estimates are extracted from measured breakthrough curves (BTCs) using a weighted nonlinear least squares (WNLS) algorithm. Optimal weights for BTCs for pulse initial conditions and continuous injections are presented. Two sample applications are analyzed: (1) pulse injection BTCs in the Selke River and (2) continuous injection laboratory experiments using natural organic matter. Model parameters are compared across models and goodness‐of‐fit metrics are presented, facilitating model evaluation. FracFitis a parameter estimation tool based on four space‐fractional and time‐fractional models used by the hydrology communityParameter estimates are extracted from measured breakthrough curves using a weighted nonlinear least squares algorithmFuture models may be implemented within the framework, allowing intercomparison of models

Shallow benthic biolayers at the top of the streambed are believed to be places of enhanced biogeochemical turnover within the hyporheic zone. They can be investigated by reactive stream tracer tests with tracer recordings in the streambed and in the stream channel. Common in‐stream measurements of such reactive tracers cannot localize where the processing primarily takes place, whereas isolated vertical depth profiles of solutes within the hyporheic zone are usually not representative of the entire stream. We present results of a tracer test where we injected the conservative tracer bromide together with the reactive tracer resazurin into a third‐order stream and combined the recording of in‐stream breakthrough curves with multidepth sampling of the hyporheic zone at several locations. The transformation of resazurin was used as an indicator of metabolism, and high‐reactivity zones were identified from depth profiles. The results from our subsurface analysis indicate that the potential for tracer transformation (i.e., the reaction rate constant) varied with depth in the hyporheic zone. This highlights the importance of the benthic biolayer, which we found to be on average 2 cm thick in this study, ranging from one third to one half of the full depth of the hyporheic zone. The reach‐scale approach integrated the effects of processes along the reach length, isolating hyporheic processes relevant for whole‐stream chemistry and estimating effective reaction rates. In‐stream tracer measurements specify bulk stream reactivity but not biolayer depthStreambed profiles identify reactive zones, but not contributions to whole‐stream reactivityCoupled in‐stream and multidepth measurements contextualize hyporheic and reach‐scale processing

The relevance of wastewater treatment plant (WWTP) effluents in fluvial networks is increasing as urbanization grows in catchments. Urban-sourced fine particles from WWTP effluents deposit and accumulate in the streambed sediment of receiving streams over time and can fuel respiration rates, which can thus potentially increase rates of biogeochemical reactions and CO2emissions to the atmosphere. We aimed to provide a quantitative assessment of the influence of WWTP-sourced fine particles deposited in the streambed sediment on stream metabolic activity for 1 year in an intermittent Mediterranean stream. More nutrient-rich and metabolically active fine particle standing stocks were observed downstream of the WWTP, propagating to the end of the 820 m study reach, especially during the dry period (i.e., when the dilution capacity of the stream to WWTP inputs is <40%). Based on the longitudinal patterns of fine particle standing stocks and their metabolic activity, we estimated that the in-stream bioreactive capacity associated with these fine particles could potentially lead to substantial carbon dioxide emissions to the atmosphere (3.1 g C/m2/d). We show the importance of incorporating fine particle standing stocks downstream of point source inputs, particularly WWTPs in intermittent streams, into carbon budgets.

Respiration of dissolved organic matter (DOM) in streams contributes to the global CO2efflux, yet this efflux has not been linked to specific DOM sources and their respective uptake rates. Further, removal of DOM inferred from longitudinal concentration gradients in river networks has been insufficient to account for observed CO2outgassing. We hypothesize that understanding in‐stream dynamics of DOM, which is a heterogeneous mixture spanning a wide range of biological labilities, requires considering that DOM lability decreases during downstream transport. To test this hypothesis, we paired seasonal bioreactor measurements of DOM biological lability with whole‐stream tracer data from White Clay Creek, Pennsylvania, USA, and used a particle‐tracking model to predict in‐stream DOM dynamics. The model simulates continuous inputs of DOM and uses storage time in the stream bioactive regions plus kinetic parameters from bioreactors to assess differential uptake of DOM fractions (i.e., fractionation) in the stream. We compared predictions for in‐stream dynamics of bulk DOM concentration (quantified as dissolved organic carbon) and fluorescent DOM components. Our model‐data synthesis approach demonstrates that more labile fractions of DOM in stream water preferentially originate and are consumed within short travel distances, causing spiraling metrics to change with downstream distance. Our model can account for local sources of rapidly cycled labile DOM, providing a basis for improved interpretation of DOM dynamics in streams that can reconcile apparent discrepancies between respiratory outgassing of CO2and longitudinal DOM concentration gradients within river networks. In streams, microorganisms metabolize naturally occurring organic molecules dissolved in streamwater and release carbon dioxide, which contributes to global carbon emissions. These organic molecules are part of a complex and diverse mixture including thousands of different chemical compounds that differ widely in susceptibility to biodegradation. We developed a mathematical model to describe changes in the pool of organic molecules flowing downstream, incorporating field and laboratory measurements of biological degradation of organic molecules and information about water flow into and out of zones that promote biological activity. We demonstrated that the molecules more susceptible to biodegradation are preferentially metabolized and become depleted over short travel distances downstream, while organic species less susceptible to biodegradation are transported farther downstream. Our model improves understanding of the transport and metabolism of organic molecules in streams, and explains factors that control the overall concentration of organic molecules in streams and rivers. The results help to reconcile discrepancies between estimates of carbon dioxide outgassing from streams and observations of organic carbon concentrations within streams. Dissolved organic matter (DOM) biological lability decreases with residence time in bioactive regions of the stream (defined as bioactive residence time)Decreasing biological lability, exchange into and residence times in bioactive regions influence in‐stream DOM dynamicsModel predictions show how the distribution of DOM fractions (i.e., fractionation) and spiraling metrics depend on in‐stream location Dissolved organic matter (DOM) biological lability decreases with residence time in bioactive regions of the stream (defined as bioactive residence time) Decreasing biological lability, exchange into and residence times in bioactive regions influence in‐stream DOM dynamics Model predictions show how the distribution of DOM fractions (i.e., fractionation) and spiraling metrics depend on in‐stream location