A common water quality issue is an excess of nutrients which can lead to problems such as eutrophication. Stream restoration is one method by which improvements in water quality may be attempted. One strategy is increasing hyporheic zone flow at baseflow by addition of instream structures. The hyporheic zone can be an area of increased biogeochemical activity, with potential enhancement of reactions such as denitrification. However, the comparative effects of various instream restoration techniques, as well as the role of watershed setting and corresponding environmental characteristics in which restoration occurs (e.g., hydraulic conductivity, stream slope), are still poorly understood. In this study we numerically modeled groundwater and surface water interaction in a 200 m second order stream reach in southwestern Virginia using MIKE SHE. We calibrated the model to hydrologic and tracer data available during field tests of restoration techniques. We then simulated different types of instream restoration techniques (e.g., fully and partially channel-spanning weirs and buried structures), and varied hydrologic and biogeochemical controlling factors driven by watershed setting. The measured effects for this sensitivity analysis were direction and magnitude of surface water-groundwater exchange and amount of denitrification. We found that factors related to watershed setting had the greatest effect on surface water-groundwater exchange and on denitrification, including streambed hydraulic conductivity, natural or background stream topography and slope, and groundwater levels. Type and number of instream structures also influenced surface water-groundwater exchange and denitrification, but to a lesser degree, and the effect of structures was in turn controlled by watershed setting. Watershed setting was thus the largest control, both on exchange overall, and the effectiveness of structures. Human effects on watersheds such as agriculture and urbanization therefore likely play a role in whether reach-scale restoration practices succeed in achieving water quality goals. More broadly, restoration efforts at the watershed scale itself, such as reducing fertilizer use or improving stormwater management, may be necessary to achieve ambitious water quality goals. Nevertheless, reach-scale restoration efforts such as in-stream structures may play a useful role in certain watershed settings. Furthermore, other reach-scale restoration techniques that affect streambed topography, such as addition of pool-riffle sequences, may be more effective, and bear investigation. / Master of Science

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Increases in reactive nitrogen from human actions have led to negative impacts on surface water (SW) and groundwater (GW) quality, and it is important to better understand denitrification processes in aquatic systems. The hyporheic zone has unique biogeochemical conditions, and is known to attenuate contaminants originating from SW and traveling through the hyporheic zone, together with necessary reactants. However, the ability of the hyporheic zone to attenuate contaminants from deeper upwelling GW plumes as they exit to SW is less understood. I used MODFLOW and SEAM3D to simulate hyporheic flow cells induced by riverbed dunes and upwelling GW together with mixing dependent denitrification of an upwelling nitrate (NO3-) plume. My basecase model scenario entailed dissolved organic carbon (DOC) and dissolved oxygen (DO) advecting from SW and DO and NO3- advecting from GW, which is typical of water in agricultural land uses. I conducted a sensitivity analysis to determine controls on mixing dependent denitrification. Mixing dependent denitrification increased with increasing hydraulic conductivity, decreasing lower bottom flux, as well as increasing DOC in SW and NO3- in GW. Non-mixing dependent denitrification also occurred when there was SW NO3-, and I found its magnitude was much greater than mixing dependent denitrification. Nevertheless, potential for hyporheic zones to attenuate upwelling NO3- plumes seems to be substantial, though highly variable depending on biogeochemical reaction rates as well as geomorphic, hydraulic and biogeochemical conditions. Stream and river restoration efforts may be able to increase both mixing and non-mixing dependent reactions by increasing hyporheic zone residence times. / Master of Science

Restoring hydrologic connectivity between the channel and floodplain is a common practice in stream and river restoration. Floodplain hydrology and hydrogeology impact biogeochemical processing and potential nutrient removal, yet rigorous field evaluations of surface and groundwater flows during overbank floods are rare. We conducted five sets of experimental floods to mimic floodplain reconnection. Experimental floods entailed pumping stream water onto an existing floodplain swale, and were conducted throughout the year to capture seasonal variation. Each set of experimental floods entailed two replicate floods occurring on successive days to test the effect of varying antecedent moisture. Water levels and specific conductivity were measured in surface water, shallow soils, and deep soils, along with surface flow into and out of the floodplain. Total flood water storage increased as vegetation density increased and or antecedent moisture decreased. Hydrologic flow mechanisms were spatially and temporally heterogeneous in surface water, in groundwater, as well as in exchange between the two and appeared to coexist in small areas. Immediate propagation of hydrostatic pressure into deep soils was suggested at some locations. Preferential groundwater flow was suggested in locations where the pressure and electrical conductivity signals propagated too fast for bulk Darcy flow through porous media. Preferential flow was particularly obvious where the pressure signal bypassed an intermediate depth but was observed at a deeper depth. Bulk Darcy flow in combination with preferential flow was suggested at locations where the flood pressure and electrical conductivity signal propagated more slowly yet arrived too quickly to be described using Darcy's Law. Finally, other areas exhibited no transmission of pressure or conductivity signals, indicating a complete lack of groundwater flow. Antecedent moisture affected the flood pulse arrival time and in some cases vertical connectivity with deeper sediments while vegetation density altered surface water storage volume. Understanding the variety of exchange mechanisms and their spatial variability will help understand the observed variability of floodplain impacts on water quality, and ultimately improve the effectiveness of floodplain restoration in reducing excess nutrient in river basins. / Master of Science

The pollution of streams and rivers is a growing concern, and environmental guidance increasingly suggests stream restoration to improve water quality. �Solute retention in off channel storage zones such as hyporheic zones and floodplains is typically necessary for significant reaction to occur. �Yet the effects of two common restoration techniques, in stream structures and inset floodplains, on solute retention have not been rigorously compared. �We used MIKE SHE to model hydraulics and solute transport in the channel, inset floodplain, and hyporheic zone of a 2nd order stream. �We varied hydraulic conditions (winter baseflow, summer baseflow, and storm flow), geology (hydraulic conductivity), and stream restoration design parameters (inset floodplain length, and presence of in stream structures). �In stream structures induced hyporheic exchange during summer baseflow with a low groundwater table (~20% of the year), while floodplains only retained solutes during storm flow conditions (~1% of the year). �Flow through the hyporheic zone increased linearly with hydraulic conductivity, while residence times decreased linearly. �Flow through inset floodplains and residence times in both the channel and floodplains increased non linearly with the fraction of bank with floodplains installed. �The fraction of stream flow that entered inset floodplains was one to three orders of magnitude higher than that through the hyporheic zone, while the residence time and mass storage in the hyporheic zone was one to five orders of magnitude larger than that in floodplain segments. �Our model results suggest that in stream structures and inset floodplains are complementary practices. / Master of Science

Increased reactive nitrogen from human activities negatively affects surface water (SW) quality. The hyporheic zone, where SW and groundwater interact, possesses unique biogeochemical conditions that can attenuate contaminants (e.g., denitrification), including mixing-dependent reactions that require components from both water sources. Previous research has explored mixing-dependent denitrification in the hyporheic zone but did not address the effects of varying SW depth as would occur from storms, tides, dam operation, and varying seasons. We simulated steady and unsteady hyporheic flow and transport through a riverbed dune using MODFLOW and SEAM3D, and varied SW depth, degree of sediment heterogeneity, amplitude and frequency of sinusoidal fluctuations, among others to determine these effects. We found that increasing steady state surface water depth from 0.1 to 1.0 m increased non-mixing dependent aerobic respiration by 270% and mixing-dependent denitrification by 78% in homogeneous sediment. Heterogeneous hydraulic conductivity fields yielded similar results, with increases in consumption due to variation in correlation length and variance of less than 5%. Daily SW fluctuation, including variation of amplitude, period, and sinusoidal versus instantaneous changes had significantly less impact than longer-term trends in SW depth. There is potential for the hyporheic zone to attenuate NO3- in upwelling groundwater plumes. Restoration efforts may be able to maximize the potential for mixing-dependent reactions in the hyporheic zone by increasing residence times. / Master of Science / Increased nitrogen in runoff from human activities negatively affects surface water quality. The hyporheic zone is where surface water and groundwater interact, and the mixing between the waters can help to this nitrogen to undergo reaction (denitrification), potentially stopping the contaminant from spreading. Previous research has explored this idea, but has not addressed the impact of varying surface water depth, as would realistically occur due to storms, tides, dam operation, and varying seasons. We simulated both constant and fluctuating surface water conditions on a riverbed dune to see the effects on hyporheic flow and denitrification. Test variables included the surface water depth, the degree of sediment heterogeneity, the amplitude and frequency of surface water fluctuations. We found that increasing the steady-state surface water depth had the most dramatic increase on the amount of reaction undergone. This trend was also seen in heterogeneous sediment. Any daily-scale surface water fluctuations, including runs that varied the amplitude, period, and sinusoidal vs instantaneous changes in surface water depth, had significantly less impact than longer-term trends in surface water depth.

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