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Many water quality and ecosystem functions performed by streams occur in the benthic biolayer, the biologically active upper (similar to 5 cm) layer of the streambed. Solute transport through the benthic biolayer is facilitated by bedform pumping, a physical process in which dynamic and static pressure variations over the surface of stationary bedforms (e.g., ripples and dunes) drive flow across the sediment-water interface. In this paper we derive two predictive modeling frameworks, one advective and the other diffusive, for solute transport through the benthic biolayer by bedform pumping. Both frameworks closely reproduce patterns and rates of bedform pumping previously measured in the laboratory, provided that the diffusion model's dispersion coefficient declines exponentially with depth. They are also functionally equivalent, such that parameter sets inferred from the 2D advective model can be applied to the 1D diffusive model, and vice versa. The functional equivalence and complementary strengths of these two models expand the range of questions that can be answered, for example, by adopting the 2D advective model to study the effects of geomorphic processes (such as bedform adjustments to land use change) on flow-dependent processes and the 1D diffusive model to study problems where multiple transport mechanisms combine (such as bedform pumping and turbulent diffusion). By unifying 2D advective and 1D diffusive descriptions of bedform pumping, our analytical results provide a straightforward and computationally efficient approach for predicting, and better understanding, solute transport in the benthic biolayer of streams and coastal sediments. U.S. NSFNational Science Foundation (NSF) [1840504, 1830172]; Virginia Tech's ICTAS EFO Opportunity Seed Investment Grant; UC Office of the President [MRP17-455083]; Compagnia di San Paolo awardCompagnia di San Paolo; U.S. DOE Biological and Environmental Research (Subsurface Biogeochemistry Research Program)United States Department of Energy (DOE); U.K. EPSRC Established Career FellowshipEngineering & Physical Sciences Research Council (EPSRC) [EP/P012027/1]; Australian Research Council (ARC) Discovery Projects funding schemeAustralian Research Council [DP120102500]; Geological Survey Water Availability and Use Science Program Funding included U.S. NSF (1840504), Virginia Tech's ICTAS EFO Opportunity Seed Investment Grant, and UC Office of the President (MRP17-455083) awards to S. B. G.; a Compagnia di San Paolo award to A. M. and F. B.; a U.S. NSF (1830172) and U.S. DOE Biological and Environmental Research (as part of the Subsurface Biogeochemistry Research Program) award to J. G.; a U.K. EPSRC Established Career Fellowship (EP/P012027/1) to I. G.; an Australian Research Council (ARC) Discovery Projects funding scheme (DP120102500) to M. G.; and support from the Geological Survey Water Availability and Use Science Program to J. H. The authors thank Andrea Bottacin-Busolin, two anonymous reviewers, and the Associate Editor for their helpful review of the manuscript, E. Gee and L. Grant for assistant with Figures 1 and 7, respectively, and M. Rippy and S. Bhide for edits. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Riverbed sediments host important biogeochemical processes that play a key role in nutrient dynamics. Sedimentary nutrient transformations are mediated by bacteria in the form of attached biofilms. The influence of microbial metabolic activity on the hydrochemical conditions within the hyporheic zone is poorly understood. We present a hydrobiogeochemical model to assess how the growth of heterotrophic and autotrophic biomass affects the transport and transformation of dissolved nitrogen compounds in bedform-induced hyporheic zones. Coupling between hyporheic exchange, nitrogen metabolism, and biomass growth leads to an equilibrium between permeability reduction and microbial metabolism that yields shallow hyporheic flows in a region with low permeability and high rates of microbial metabolism near the stream-sediment interface. The results show that the bioclogging caused by microbial growth can constrain rates and patterns of hyporheic fluxes and microbial transformation rate in many streams.

Benthic (streambed) biofilms metabolize a substantial fraction of particulate organic matter and nutrient inputs to streams. These microbial communities comprise a significant proportion of overall biomass in headwater streams, and they present a primary control on the transformation and export of labile organic carbon. Biofilm growth has been linked to enhanced fine particle deposition and retention, a feedback that confers a distinct advantage for the acquisition and utilization of energy sources. We quantified the influence of biofilm structure on fine particle deposition and resuspension in experimental stream mesocosms. Biofilms were grown in identical 3-m recirculating flumes over periods of 18-47 days to obtain a range of biofilm characteristics. Fluorescent, 8-μm particles were introduced to each flume, and their concentrations in the water column were monitored over a 30-minute period. We measured particle concentrations using a flow cytometer and mesoscale (10 μm to 1 cm) biofilm structure using optical coherence tomography. Particle deposition-resuspension dynamics were determined by fitting results to a stochastic mobile-immobile model, which showed that retention timescales for particles within the biofilm-covered streambeds followed a power-law residence time distribution. Particle retention times increased with biofilm areal coverage, biofilm roughness, and mean biofilm height. Our findings suggest that biofilm structural parameters are key predictors of particle retention in streams and rivers. This article is protected by copyright. All rights reserved.

Fifty years of hyporheic zone research have shown the important role played by the hyporheic zone as an interface between groundwater and surface waters. However, it is only in the last two decades that what began as an empirical science has become a mechanistic science devoted to modeling studies of the complex fluid dynamical and biogeochemical mechanisms occurring in the hyporheic zone. These efforts have led to the picture of surface-subsurface water interactions as regulators of the form and function of fluvial ecosystems. Rather than being isolated systems, surface water bodies continuously interact with the subsurface. Exploration of hyporheic zone processes has led to a new appreciation of their wide reaching consequences for water quality and stream ecology. Modern research aims toward a unified approach, in which processes occurring in the hyporheic zone are key elements for the appreciation, management, and restoration of the whole river environment. In this unifying context, this review summarizes results from modeling studies and field observations about flow and transport processes in the hyporheic zone and describes the theories proposed in hydrology and fluid dynamics developed to quantitatively model and predict the hyporheic transport of water, heat, and dissolved and suspended compounds from sediment grain scale up to the watershed scale. The implications of these processes for stream biogeochemistry and ecology are also discussed.

[1] Water exchange between streams and hyporheic zones is highly dynamic, and its temporal variation is related to the hydrologic fluctuations of stream discharge and groundwater levels. Unfortunately, predictions of temporal patterns of exchange are difficult due to the many hydrodynamic and morphodynamic processes that are involved and also to their complex nonlinear interactions. Examples of these processes include the evolution of streambed morphology in response to changing streamflow as well as the feedback on surface flow induced by drag resistance due to evolving bed forms. In this work, we have employed a stochastic method to analyze the temporal dynamics of bed form-driven hyporheic exchange in a stream characterized by subcritical flow and daily discharge variations. The method is an extension of previous studies that includes current-induced alterations of bedform size and celerity and their effect on water exchange. The modeling results show that during high flows, stream water penetrates deeper and for longer times in the sediments. At the same time, the predicted rate of water exchange per unit streambed area decreases because the streambed area occupied by each bed form increases faster than the volumetric rate of stream water exchange induced by the same bed form. This reduction can be compensated by the increase in wetted area with discharge, which may provide additional streambed area for water exchange. One the main finding of the study is that the time-averaged values of exchange flux and depths are quite similar to those modeled for a steady mean discharge, while residence times are somewhat lower. Predicted temporal variations of exchange depths and times around their time-averaged values are moderate compared to steady state values.

[1] Aquatic sediment hosts coupled pore water flow and biogeochemical reactions that mediate water quality across the fluvial corridor including adjacent alluvial aquifers. However, the effect of small-scale variations in sediment hydraulic properties on nutrient transformation occurring within the sediment is poorly understood. We show through numerical flow and transport simulations, for two realistic heterogeneous permeability cases typical of lowland rivers and two idealized homogeneous ones, that there is little difference in the reactive transport fields, the bulk reaction rates, and nutrient sink/source function despite stark differences in flow fields. This is because the reactions are ultimately controlled by characteristic or bulk residence times that are similar for the heterogeneous and homogeneous cases. This is a promising result for predictive models based solely on relative ratios of residence times and reactive time scales.

[1] The interest about the exchange of water between streams and aquifers has been increasing among the hydrologic community because of the implications of the exchange of heat, solutes, and colloids for the water quality of aquatic environments. Unfortunately, our understanding of the relevance of the exchange processes is limited by the great number of coupled hydrological and geomorphological factors that interact to generate the complex spatial patterns of exchange. In this context, the present work presents a mathematical model for the surface-subsurface exchange through the streambed of a meandering stream. The model is based on the linearization of the equations that govern the hydrodynamics and the morphodynamics of the system, and it provides a first-order analytical solution of the coupled flow field of both the surface and the subsurface flows. The results show that stream curvature determines a characteristic spatial pattern of hyporheic exchange, with water upwelling and downwelling concentrated near the stream banks. The exchange can drive surface water deep into the sediments, thus keeping deep alluvium regions connected with the stream. The relationships between hyporheic exchange flux and the geometrical and hydrodynamical properties of the stream-aquifer system are also investigated.

[1] The dynamics of chemicals within a catchment are strongly affected by the exchange between surface water and groundwater. The activity of hyporheic microorganisms plays a key role in these processes, as they are able to oxidize and reduce organic matter and nutrients. The interplay between the residence times in the hyporheic zone and the temporal scales of the microbial reactions must thus be understood in order to improve our understanding of the role of fluvial environments in nutrient cycling. In this paper we focus on the intrameander hyporheic region and investigate the links between river morphology, hyporheic flow field, and biogeochemical processes. We adopt a modeling framework that considers the planimetric evolution of a meandering river, the hyporheic flow field induced by the river sinuosity, and the main biogeochemical reactions of organic carbon degradation. The chemical zonation of the intrameander hyporheic zone clearly emerges as a result of the coupling between hyporheic flow and biochemical activity. The resulting patterns of nutrient concentrations are strongly influenced by the river morphology. We also show how to estimate the characteristic timescales of the redox reactions and that their interplay with the kinematic timescales of the hyporheic flow controls both the biochemical zonation and the overall rate of nutrient transformation.

[1] Several geomorphological fluvial features are able to induce hyporheic exchange between the rivers and the alluvial sediments. However, while the small-scale exchange induced by bed forms has been thoroughly investigated, the role of the larger features remains poorly understood. Here, we focus on the hyporheic flows driven by the channel sinuosity in the intrameander zone. A physically based model is adopted to simulate the morphodynamic evolution of three different meandering rivers, from the first stages of the meander evolution until the incipient meander cutoff. For each stage, the sinuosity-driven intrameander hyporheic flow is computed. In this way, the hyporheic flow field, the fluxes exchanged with the river, and the residence times are described during the whole meander evolution. The main result concerns the existence of a remarkable zonation induced by the flow field in the intrameander zone. The more the meander evolves, the more the zonation becomes pronounced, and the probability distribution of the residence times shows a bimodal shape with an intermediate power law behavior. Some general rules governing the typical timescales of the intrameander hyporheic flow and the mean exchanged flux are also deduced.

[1] Pore water in stream sediments is continuously exchanged with the surface water from the overlying stream. This exchange of water and solutes that occurs across the stream-sediment interface plays an important role for fluvial ecology because of the unique biochemical conditions, rich biodiversity, and high rates of metabolism. While many studies have observed the extent of the hyporheic zone to be modified by changes in the level of the groundwater table, the actual importance of this interaction is still difficult to quantify. Here, we focus on the case of bedform induced hyporheic exchange to show how the the volume of hyporheic sediments that receive water from the stream is significantly reduced by the upwelling of subsurface water. A simple scaling relationship for the assessment of maximum depth of the hyporheic zone is proposed by relating hyporheic flow to the groundwater discharge in an aquifer with given hydraulic properties and head difference between the stream and the aquifer.

[1] The transport of solutes in rivers is influenced by the exchange of water between the river and the underlying hyporheic zone. The residence times of solutes in the hyporheic zone are typically much longer than traveltimes in the stream, resulting in a significant delay in the downstream propagation of solutes. A new model for this process is proposed here on the basis of the continuous time random walk (CTRW) approach. The CTRW is a generalization of the classic random walk that can include arbitrary distributions of waiting times, and it is particularly suited to deal with the long residence times arising from hyporheic exchange. Inclusion of suitable hyporheic residence time distributions in the CTRW leads to a generalized advection-dispersion equation for in-stream concentration breakthrough curves that includes the effects of specific hyporheic exchange processes. Here examples are presented for advective hyporheic exchange resulting from regular and irregular series of bedforms. A second major advantage of the CTRW approach is that the combined effects of different processes affecting overall downstream transport can be incorporated in the model by convolving separate waiting time distributions for each relevant process. The utility of this approach is illustrated by analyzing the effects of local-scale sediment heterogeneity on bedform-induced hyporheic exchange. The ability to handle arbitrarily wide residence time distributions and the ability to assess the combined effects of multiple transport processes makes the CTRW model framework very useful for the study of solute transport problems in rivers. The model presented here can be easily extended to represent different types of surface-subsurface exchange processes and the transport of both conservative and nonconservative substances in rivers.

[1] A model for the evaluation of the intra-meander hyporheic exchange fluxes is presented. The method relies on a physically-based morphodynamic model to predict the characteristics of the flow field in a meandering river and the temporal evolution of its planimetry. The hyporheic fluxes induced at the meander scale by the river sinuosity can therefore be computed. The application of the model to a simulated case has shown the fundamental role of the river planimetry on the hyporheic exchange pattern at the meander scale, and its influence on the long-term evolution of the hyporheic exchange. Citation: Boano, F., C. Camporeale, R. Revelli, and L. Ridolfi (2006), Sinuositydriven hyporheic exchange in meandering rivers, Geophys. Res. Lett., 33, L18406, doi:10.1029/2006GL027630.

[1] The geostatistical method, formulated in the groundwater field, has been applied to identify contaminant sources in river pollution problems. The problem consists of recovering a contaminant source at a known location from a finite number of concentration measurements. It is an ill-posed problem, whose solution is nonunique and cannot be determined through standard techniques. The presence of dead zones has been considered because of their relevant influence on transport processes. The possibility of linear decay reactions in the main stream and in the dead zones has also been included. Applications to field data show that the method is efficient in recovering the release history of an arbitrarily distributed source as well as multiple independent point sources, given a finite number of observed concentrations at one or several downstream points. The influence of the degree of dispersion on the observations is stressed. Finally, the effects of measurement errors and of the number of measurement points have been investigated.