Daniele Tonina

Hyporheic exchange in gravel bed rivers with pool-riffle morphology : Laboratory experiments and three-dimensional modeling

Received 7 June 2005; revised 30 June 2006; accepted 25 August 2006; published 31 January 2007. [1] We report the first laboratory simulations of hyporheic exchange in gravel pool-riffle channels, which are characterized by coarse sediment, steep slopes, and three-dimensional bed forms that strongly influence surface flow. These channels are particularly important habitat for salmonids, many of which are currently at risk worldwide and which incubate their offspring within the hyporheic zone. Here we perform a set of laboratory experiments examining the effects of discharge and bed form amplitude on hyporheic exchange, with surface-subsurface mixing measured directly from the concentration decay of a conservative tracer (fluorescein) injected into the surface flow. Near-bed pressure measurements were also used to predict hyporheic exchange from a three-dimensional pumping transport model. Comparison of the predicted and observed hyporheic exchange shows good agreement, indicating that the major mechanism for exchange is bed form–induced advection. However, the effect of bed forms is modulated by discharge and the degree of topographic submergence. We also tested the performance of the hydrostatic pressure as a proxy for the observed near-bed pressure in driving hyporheic exchange, which would facilitate field measurement and analysis of hyporheic flow in natural rivers. We found agreement with measured hyporheic exchange only for low bed form amplitudes and high flows.

Remote Sensing of Channels and Riparian Zones with a Narrow-Beam Aquatic-Terrestrial LIDAR

The high-resolution Experimental Advanced Airborne Research LIDAR (EAARL) is a new technology for cross-environment surveys of channels and floodplains. EAARL measurements of basic channel geometry, such as wetted cross-sectional area, are within a few percent of those from control field surveys. The largest channel mapping errors are along stream banks. The LIDAR data adequately support 1D and 2D computational fluid dynamics models and frequency domain analyses by wavelet transforms. Further work is needed to establish the stream monitoring capability of the EAARL and the range of water quality conditions in which this sensor will accurately map river bathymetry.

Solutions for the diurnally forced advection-diffusion equation to estimate bulk fluid velocity and diffusivity in streambeds from temperature time series

[1] Work over the last decade has documented methods for estimating fluxes between streams and streambeds from time series of temperature at two depths in the streambed. We present substantial extension to the existing theory and practice of using temperature time series to estimate streambed water fluxes and thermal properties, including (1) a new explicit analytical solution to predict one-dimensional fluid velocity from amplitude and phase information; (2) an inverse function, also with explicit formulation; (3) methods to estimate fluid velocity from temperature measurements with unknown depths; (4) methods to estimate thermal diffusivity from the temperature time series when measurement depths are known; (5) methods to track streambed elevation between two sensors, given knowledge of the thermal diffusivity from (4) above; (6) methods to directly calculate the potential error in velocity estimates based on the measurement error characteristics ; and (7) methods for validation of parameter estimates. We also provide discussion and theoretical insights developed from the solutions to better understand the physics and scaling of the propagation of the diurnal temperature variation through the streambed. In particular, we note that the equations developed do not replace existing equations applied to the analysis, rather they are new equations representing new aspects of the process, and, as a consequence, they increase the amount of information that can be derived from a particular set of thermal measurements.

A three-dimensional model for analyzing the effects of salmon redds on hyporheic exchange and egg pocket habitat

A three-dimensional fluid dynamics model is developed to capture the spatial complexity of the effects of salmon redds on channel hydraulics, hyporheic exchange, and egg pocket habitat. We use the model to partition the relative influences of redd topography versus altered hydraulic conductivity (winnowing of fines during spawning) on egg pocket conditions for a simulated pool–riffle channel with a redd placed at the pool tail. Predictions show that altered hydraulic conductivity is the primary factor for enhancing hyporheic velocities and dissolved oxygen content within the egg pocket. Furthermore, the simulations indicate that redds induce hyporheic circulation that is nested within that caused by pool–riffle topography and that spawning-related changes in hyporheic velocities and dissolved oxygen content could create conditions suitable for incubation in locations that otherwise would be unfavorable (reinforcing the notion that salmonids actively modify their environment in ways that may be beneficial ...

Semianalytical analysis of hyporheic flow induced by alternate bars

[1] We investigate the effects of alternate bar morphology on the hyporheic flow in gravel bed rivers. Our goal is to investigate the relations between residence time distribution of a conservative tracer and the parameters controlling bed form morphology. We assume homogeneous, isotropic or anisotropic hydraulic properties of the streambed sediment and constant flow regime in equilibrium with the bed form, which is considered fixed because its formation timescale is much longer than that of the subsurface flow. Under these assumptions, we solve the in‐stream and hyporheic flow fields analytically in a three‐dimensional domain. We approximate the former with the shallow water equations and model the latter as a Darcian flow. The two systems are linked through the hydraulic head distribution, which is predicted at the streambed by the surface model and applied as a boundary condition to the hyporheic flow model. We solve the solute transport equation in the hyporheic zone for a conservative tracer by means of particle tracking. Our model predicts that the mean value and variance of the hyporheic residence time depend on the alternate bar amplitude at equilibrium. This result is found to be applicable also to discharges that are lower (70% in our simulations) than the formative and submerge the bars entirely. Moreover, our analysis shows that 95% of the hyporheic flow is confined in a near‐bed layer, whose depth is about the width of the channel and shallows from low to steep gradient streams. This causes the hyporheic mean residence time to reach a threshold when the alluvial depth is deeper than the channel width. Our results also show that as the stream slope increases, the streamlines compact near to the streambed, thereby reducing the mean residence time and its variance. Finally, we observe that the hyporheic residence time of pulse injections of passive solutes is lognormally distributed, with the mean value depending in a simple manner on the amplitude of the alternate bars.

A hydrologic model demonstrates nitrous oxide emissions depend on streambed morphology

Rivers are hot spots of nitrous oxide (N2O) emissions due to denitrification. Although the key role of rivers in transforming reactive inorganic nitrogen is widely recognized, the recent estimates of N2O emissions by the Intergovernmental Panel on Climate Change (IPCC) may be largely underestimated. This denotes a lack of reliable and robust methodologies to upscale denitrification, and other biogeochemical processes, from the local to the network scale. Here we demonstrate that stream hydromorphology strongly influences N2O emissions. We provide an integrative methodology for upscaling local biogeochemical processes to the catchment scale with a Damkohler number, which accounts for the complex interplay between stream hydromorphology and biogeochemical characteristics of streambed sediments. Application of this theoretical framework to the large data set collected as part of the second Lotic Intersite Nitrogen eXperiment (LINXII) demonstrates that stream morphology is a key factor controlling emissions of N2O from streams.

Effects of bathymetric lidar errors on flow properties predicted with a multi‐dimensional hydraulic model

New remote sensing technologies and improved computer performance now allow numerical flow modeling over large stream domains. However, there has been limited testing of whether channel topography can be remotely mapped with accuracy necessary for such modeling. We assessed the ability of the Experimental Advanced Airborne Research Lidar, to support a multi-dimensional fluid dynamics model of a small mountain stream. Random point elevation errors were introduced into the lidar point cloud, and predictions of water surface elevation, velocity, bed shear stress, and bed mobility were compared to those made without the point errors. We also compared flow model predictions using the lidar bathymetry with those made using a total station channel field survey. Lidar errors caused < 1 cm changes in the modeled water surface elevations. Effects of the point errors on other flow characteristics varied with both the magnitude of error and the local spatial density of lidar data. Shear stress errors were greatest where flow was naturally shallow and fast, and lidar errors caused the greatest changes in flow cross-sectional area. The majority of the stress errors were less than ± 5 Pa. At near bankfull flow, the predicted mobility state of the median grain size changed over ≤ 1.3% of the model domain as a result of lidar elevation errors and ≤ 3% changed mobility in the comparison of lidar and ground-surveyed topography. In this riverscape, results suggest that an airborne bathymetric lidar can map channel topography with sufficient accuracy to support a numerical flow model.

Development of a spatially-distributed hydroecological model to simulate cottonwood seedling recruitment along rivers.

Dam operations have altered flood and flow patterns and prevented successful cottonwood seedling recruitment along many rivers. To guide reservoir flow releases to meet cottonwood recruitment needs, we developed a spatially-distributed, GIS-based model that analyzes the hydrophysical requirements for cottonwood recruitment. These requirements are indicated by five physical parameters: (1) annual peak flow timing relative to the interval of seed dispersal, (2) shear stress, which characterizes disturbance, (3) local stage recession after seedling recruitment, (4) recruitment elevation above base flow stage, and (5) duration of winter flooding, which may contribute to seedling mortality. The model categorizes the potential for cottonwood recruitment in four classes and attributes a suitability value at each individual spatial location. The model accuracy was estimated with an error matrix analysis by comparing simulated and field-observed recruitment success. The overall accuracies of this Spatially-Distributed Cottonwood Recruitment model were 47% for a braided reach and 68% for a meander reach along the Kootenai River in Idaho, USA. Model accuracies increased to 64% and 72%, respectively, when fewer favorability classes were considered. The model predicted areas of similarly favorable recruitment potential for 1997 and 2006, two recent years with successful cottonwood recruitment. This model should provide a useful tool to quantify impacts of human activities and climatic variability on cottonwood recruitment, and to prescribe instream flow regimes for the conservation and restoration of riparian woodlands.

Role of surface and subsurface processes in scaling N2O emissions along riverine networks

Significance We show that N2O emissions from riverine systems depend on river and stream size and that the primary source of N2O production shifts from the hyporheic and benthic zones in streams to the benthic and water column in rivers. This analysis also reveals the primary scaling factors governing riverine N2O emissions. Finally, it provides a predictive tool to quantify N2O emissions from any riverine environment worldwide, among biomes, land-use types, and climatic conditions, using readily available reach-scale biogeochemical measurements and hydromorphological data. Riverine environments, such as streams and rivers, have been reported as sources of the potent greenhouse gas nitrous oxide (N2O) to the atmosphere mainly via microbially mediated denitrification. Our limited understanding of the relative roles of the near-surface streambed sediment (hyporheic zone), benthic, and water column zones in controlling N2O production precludes predictions of N2O emissions along riverine networks. Here, we analyze N2O emissions from streams and rivers worldwide of different sizes, morphology, land cover, biomes, and climatic conditions. We show that the primary source of N2O emissions varies with stream and river size and shifts from the hyporheic–benthic zone in headwater streams to the benthic–water column zone in rivers. This analysis reveals that N2O production is bounded between two N2O emission potentials: the upper N2O emission potential results from production within the benthic–hyporheic zone, and the lower N2O emission potential reflects the production within the benthic–water column zone. By understanding the scaling nature of N2O production along riverine networks, our framework facilitates predictions of riverine N2O emissions globally using widely accessible chemical and hydromorphological datasets and thus, quantifies the effect of human activity and natural processes on N2O production.

Does small‐bodied salmon spawning activity enhance streambed mobility?

Female salmonids bury and lay their eggs in streambeds by digging a pit, which is then covered with sediment from a second pit that is dug immediately upstream. The spawning process alters streambed topography, winnows fine sediment, and mixes sediment in the active layer. The resulting egg nests (redds) contain coarser and looser sediments than those of unspawned streambed areas, and display a dune-like shape with an amplitude and length that vary with fish size, substrate conditions, and flow conditions. Redds increase local bed surface roughness (<10−1 channel width, W), but may reduce the size of macro bedforms by eroding reach-scale topography (100–101W). Research has suggested that spawning may increase flow resistance due to redd form drag, resulting in lower grain shear stress and less particle mobility. Spawning, also prevents streambed armoring by mixing surface and subsurface material, potentially increasing particle mobility. Here we use two-dimensional hydraulic modeling with detailed prespawning and postspawning bathymetries and field observations to test the effect of spawning by small-bodied salmonids on sediment transport. Our results show that topographical roughness from small salmon redds has negligible effects on shear stress at the reach-unit scale, and limited effects at the local scale. Conversely, results indicate sediment mixing reduces armoring and enhances sediment mobility, which increases potential bed load transport by subsequent floods. River restoration in fish-bearing streams should take into consideration the effects of redd excavation on channel stability. This is particularly important for streams that historically supported salmonids and are the focus of habitat restoration actions.