Thesis (M.S.)--University of Nevada, Reno, 2006. / "December, 2006." Includes bibliographical references. Online version available on the World Wide Web.

Thesis (M.S.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 113-118). Also available on the World Wide Web.

Streams and rivers are a vital part of our ecosystem. They are imperiled by human ecological activities such as urbanization, industrialization, and agriculture which discharge excess nitrate and other pollutants into our waterways. Here, this dissertation seeks to understand the physical and biogeochemical processes which attenuate pollutants in stream corridors. The focus is hyporheic zones which form the interface between surface water and groundwater below and adjacent to stream channels, and riparian zones which form the interface between channels and adjacent uplands, both of which can attenuate pollutants. In this context, soil-pipes can dominate subsurface hydraulics. This research first employed MODFLOW and MT3D-USGS to model transient hyporheic hydraulics and nitrate transport in a length of riparian/riverbank soil to probe the effects of soil pipes on hydraulics and denitrification due to peak flow events in the channel. Findings showed that inserting just one soil pipe 1.5 m in length caused a ~75% increase in both hyporheic exchange and denitrification. A rough upscaling showed soil pipes could remove up to ~3% of nitrate along a 1-km reach. Next, the ability of soil pipes to bypass the often championed ability of riparian buffers to remove nitrate migrating from uplands to the channel was evaluated. This effort also employed MODFLOW and MT3D-USGS to simulated hydraulics and nitrate removal along a length of riparian soil. Findings showed that soil pipes increased flow of nitrate to the banks by five orders of magnitude in some cases. We posited a non-dimension parameter which governs when nitrate bypass is significant. In addition to soil pipes, dune bedforms can also enhance hyporheic exchange, primarily in the stream/riverbed. Again employing MODFLOW but now pairing with the transport code SEAM3D to simulate microbially-mediated aerobic metabolism of dissolved organic carbon and dissolved oxygen, the combined effects of dune translation and microbial growth and death were explored. Major findings include that neglecting microbial growth can lead to inaccurate modeling of biogeochemistry, and that aerobic metabolism increased with celerity. The results herein bolster knowledge of natural pollutant attenuation in stream and river corridors, and have implications for pollutant mitigation strategy and stream credit allocation. / Doctor of Philosophy / Streams are a vital part of our ecosystem. They are imperiled by human ecological activities such as urbanization, industrialization, and agriculture which discharge nitrate and other pollutants into our waterways. Here, this dissertation seeks to understand the physical and biological processes which attenuate pollutants. The hyporheic zone is the interface between surface water and groundwater below the bed and adjacent to stream banks, and can attenuate pollutants. Transient peak flow events such as a storm or snow melt raise the stream water levels, causing the water pressure in the stream channel to temporarily outweigh the water pressure in the soil pore spaces adjacent to the stream channel. This drives water into the banks subjecting it to pollutant attenuation processes. Soil pipes (long cylindrical void spaces created by decayed plant roots) are prevalent along stream banks, and they dominate subsurface hydraulics. This dissertation implemented a numerical study on a chunk of riparian soil to probe the effects of soil pipes on hydraulics and denitrification. Findings showed that inserting just one – 1.5 m soil pipe caused a ~75% increase in both water flow volume into the bank and nitrate removal. Riparian buffers are the vegetated strips adjacent to stream channels and have long been championed as stalwarts of pollutant removal. Soil pipes undermine this by acting as a bypass mechanism. A numerical study was again performed on a chunk of riparian soil to quantify the effects soil pipes on riparian bypass of nitrate. Findings showed that soil pipes increased flow of nitrate to the banks by five orders of magnitude in some cases. This means that a buffer enhancement strip with fine roots that prevent the formation of soil pipes should be installed along riparian buffers. In addition to soil pipes, dune bedforms can increase flowrate of water into the hyporheic zone. This dissertation modeled the combined effects of dune translation and microbial growth and death. Major findings include that neglecting microbial growth can lead to inaccurate modeling of biogeochemistry, and that biodegradation increases with increased dune velocity. The results herein bolster knowledge on natural pollutant attenuation in streams, and have implications in terms of pollutant mitigation strategy and stream credit allocation.

The feedbacks between hydrology and biogeochemical cycling of nitrogen (N) are of critical importance to global bioavailable N budgets. Human activities are dramatically increasing the amount of bioavailable N in the biosphere, which is causing increasingly frequent and severe impacts on ecosystems and human welfare. Streams are important features in the landscape for N cycling, because they integrate many sources of terrestrially derived N and control export to downgradient systems via internal source and sink processes. N transformations in stream ecosystems are typically very complex due to spatiotemporal variability in the factors controlling N biogeochemistry. Thus, it is difficult to predict if a particular stream system will function as a net source or sink of bioavailable N. A key location for N transformations in stream ecosystems is the hyporheic zone, where stream and ground waters mix. The hyporheic zone can be a source of bioavailable N via nitrification or a sink via denitrification. These N transformations are regulated by the physical and biogeochemical conditions of hyporheic zones. Natural heterogeneity in streams leads to unique combinations of both the physical and biogeochemical conditions which in turn result in unique N source and sink conditions. This dissertation investigates the relationships between physical and biogeochemical controls and the resulting fate of bioavailable N in hyporheic zones. The key physical factor investigated is the supply rate of solutes which is a function of transport processes - advection and dispersion, and transport conditions - hydraulic conductivity and flowpath length. Different physical conditions result in different characteristic residence times of water and solutes in hyporheic zones. The key biogeochemical factors investigated are the dynamics of oxygen (O₂), labile dissolved organic carbon (DOC), and inorganic bioavailable N (NH₄⁺ and NO₃⁻). This dissertation uses ¹⁵N isotope experiments, numerical modeling of coupled transport of the bioavailable N species, O₂ and DOC, and a suite of geophysical measurements to identify the key linkages between hydrological and biogeochemical controls on N transformations in hyporheic zones. Specifically, it was determined that the conditions governing the fate of hyporheic N are both the physical transport and reaction kinetics – the residence time of water and the O2 uptake rate. An important scaling relationship is developed by relating the characteristic timescales of residence time and O₂ uptake. The resulting dimensionless relationship, the Damköhler number for O₂, is useful for scaling different streams hyporheic zones and their role on stream N source – sink dynamics. More generally, these investigations demonstrate that careful consideration and quantification of hydrological processes can greatly inform the investigation of aquatic biogeochemical dynamics and lead to the development of process-based knowledge. In turn, this process-based knowledge will facilitate more robust approaches to quantifying and predicting biogeochemical cycles and budgets. / Graduation date: 2012 / Access restricted to the OSU Community at author's request from Sept. 21, 2011 - March 21, 2012

Surface transient storage (STS) in stream ecosystems serve an important function in retaining nutrients and refugia for aquatic communities. Unfortunately, they can retain contaminants as well. Therefore, it is of importance to determine the residence time distribution (RTD). A RTD of a particular STS zone encompasses the time it takes for the first pulse of water to leave the STS zone, and for the mean residence time of water in that zone, among other things. The RTD of STS is also useful to subtract from the RTD of the total transient storage in streams in order to determine the hyporheic transient storage (HTS) of streams, which is difficult to measure. Currently, there is no definitive method of determining the RTD of STS. They have been determined with tracer injection alone, though this is time consuming and subject to interference from HTS. A relationship between STS physical characteristics and a RTD would be desirable, as this would characterize the time of entrainment of STS based upon a few easily measured physical parameters. This exists for groyne fields and flumes, which both have artificial STS. However, direct application of these equations to natural STS leads to errors due to simplistic geometries. The focus of this study determines RTDs in lateral STS, which is adjacent to the main channel of a stream and a significant proportion of STS, and its relationship to physically measurable parameters of lateral STS. Twenty sites throughout Oregon were each injected with NaCl to determine four residence timescales: Langmuir time (��[subscript L]), negative inverse slope of the normalized concentration curve of the primary gyre (��[subscript 1]), negative inverse slope of the normalized concentration curve of the entire STS zone (��[subscript 2]), and the mean residence time (��[subscript STS]). The RTDs of these sites were then compared to the length, width, and depth of each lateral STS zone, as well as the velocity of the adjacent main channel. This data also was used to calculate dimensionless parameters submergence, a measure of bed roughness, and k, a measure of exchange that relates ��STS to lateral STS and associated parameters. ��[subscript 1] was found to be identical to ��[subscript STS], and ��[subscript 2] could not be defined. ��[subscript STS] was found to be approximately 1.35 times ��[subscript L], the ratio of which (��[subscript L]/��[subscript STS]) is positively correlated with lateral STS submergence. ��[subscript L] and ��[subscript STS] are positively correlated with lateral STS parameters, and inversely correlated with main channel velocity. The value of k from this study was comparable to the value of k from other studies in flumes, and so there is a relationship between RTDs and lateral STS parameters. / Graduation date: 2013