Erin N. Bray

California’s mining legacy continues to threaten water quality and ecosystem health throughout the state. This study focuses on mercury (Hg) releases from the former New Idria Mercury Mine, which was the second largest historic Hg producer in North America. San Carlos Creek, which flows adjacent to the mine, is impacted by acid mine drainage (AMD) as well as mining waste piles that sit at a high angle of repose over the channel. We documented total mercury (HgT) concentrations exceeding California’s 50 ng L^-1 water quality objective for almost 10 km, from New Idria to a ~ 0.25 km² perennial wetland at the confluence of San Carlos Creek and Silver Creek within the Panoche Creek watershed. During baseflow and low flow storm conditions, unfiltered total Hg (U-HgT) in creek water downstream from the mine typically ranged from 1,100–9,200 ng Hg L^-1, with >90% of Hg in the particulate phase. U-HgT correlated (R² = 0.6) with suspended particulate matter (SPM) that was presumably a mixture of AMD-derived flocculant, weathered calcines (i.e., roasted ore), and sediment from the local watershed. The flocculant is easily resuspended in baseflow conditions and scoured from the channel during high flow events, resulting in seasonal patterns of Hg transport in San Carlos Creek that do not always align with the stream hydrograph. Mercury from New Idria, along with AMD flocculant, metals, sulfate, and other anions, presumably accumulate or infiltrate at the Silver Creek wetland until larger storms remobilize sediments further downstream towards the ~ 0.65 km² Panoche Creek Wetland, the Panoche Fan, and ultimately to the Fresno Slough, Mendota Wildlife Area, Mendota Pool and San Joaquin River.

Large‐scale river restoration programs have emerged recently as a tool for improving spawning habitat for native salmonids in highly altered river ecosystems. Few studies have quantified the extent to which restored habitat is utilized by salmonids, which habitat features influence redd site selection, or the persistence of restored habitat over time. We investigated fall‐run Chinook salmon spawning site utilization and measured and modeled corresponding habitat characteristics in two restored reaches: a reach of channel and floodplain enhancement completed in 2013 and a reconfigured channel and floodplain constructed in 2002. Redd surveys demonstrated that both restoration projects supported a high density of salmon redds, 3 and 14 years following restoration. Salmon redds were constructed in coarse gravel substrates located in areas of high sediment mobility, as determined by measurements of gravel friction angles and a grain entrainment model. Salmon redds were located near transitions between pool‐riffle bedforms in regions of high predicted hyporheic flows. Habitat quality (quantified as a function of stream hydraulics) and hyporheic flow were both strong predictors of redd occurrence, though the relative roles of these variables differed between sites. Our findings indicate that physical controls on redd site selection in restored channels were similar to those reported for natural channels elsewhere. Our results further highlight that in addition to traditional habitat criteria (e.g., water depth, velocity, and substrate size), quantifying sediment texture and mobility, as well as intragravel flow, provides a more complete understanding of the ecological benefits provided by river restoration projects.

Along many rivers, dams trap sediment and water released from the dams is clear. Downstream of the dam, temperature variability along the river is controlled by climate that warms or cools the water, the flow magnitude, and the spectral properties of water and the river's bed. Using field observations, a synoptic numerical model without calibration couples a full‐spectrum radiation balance with turbulent heat fluxes, bed conduction, and a hydraulic model that estimates depth and velocity. We show that variations in the river's temperature are sensitive to the albedo of the sediment on the bed, especially at shallow depths and smaller discharges. However, about half the solar radiation lies in a spectral range where water is highly absorptive; in these wavelengths, absorption is independent of depth. In spring and summer with many hours of sunlight, releases of cold water will have limited influence on temperatures beyond tens of kilometers downstream of a dam.

Geomorphic and hydraulic processes, which form gravel bars in large lowland rivers, have distinctive characteristics that control the magnitude and spatial patterns of infiltration and exfiltration between rivers and their immediate subsurface environments. We present a bedform‐infiltration relation together with a set of field measurements along two reaches of the San Joaquin River, CA to illustrate the conditions required for infiltration and exfiltration of flow between a stream and its undulating bed, and a numerical model to investigate the factors that affect paths and residence times of flow through barforms at different discharges. It is shown that asymmetry of bar morphology is a first‐order control on the extent and location of infiltration, which would otherwise produce equal areas of infiltration and exfiltration under the assumption of sinusoidal bedforms. Hydraulic conductivity varies by orders of magnitude due to fine sediment accumulation and downstream coarsening related to the process of bar evolution. This systematic variability not only controls the magnitude of infiltration, but also the residence time of flow through the bed. The lowest hydraulic conductivity along the reach occurred where the difference between the topographic gradient and the water‐surface gradient is at a maximum and thus where infiltration would be greatest into a homogeneous bar, indicating the importance of managing sand supply to maintain the ventilation and flow through salmon spawning riffles. Numerical simulations corroborate our interpretation that infiltration patterns and rates are controlled by distinctive features of bar morphology.

The question: ‘how does a streambed change over a minor flood?’ does not have a clear answer due to lack of measurement methods during high flows. We investigate bedload transport and disentrainment during a 1.5‐year flood by linking field measurements using fiber optic distributed temperature sensing (DTS) cable with sediment transport theory and an existing explicit analytical solution to predict depth of sediment deposition from amplitude and phase changes of the diurnal near‐bed pore‐water temperature. The method facilitates the study of gravel transport by using near‐bed temperature time series to estimate rates of sediment deposition continuously over the duration of a high flow event coinciding with bar formation. The observations indicate that all gravel and cobble particles present were transported along the riffle at a relatively low Shields Number for the median particle size, and were re‐deposited on the lee side of the bar at rates that varied over time during a constant flow. Approximately 1–6% of the bed was predicted to be mobile during the 1.5‐year flood, indicating that large inactive regions of the bed, particularly between riffles, persist between years despite field observations of narrow zones of local transport and bar growth on the order ~3–5 times the median particle size. In contrast, during a seven‐year flood approximately 8–55% of the bed was predicted to become mobile, indicating that the continuous along‐stream mobility required to mobilize coarse gravel through long pools and downstream to the next riffle is infrequent. Copyright © 2017 John Wiley & Sons, Ltd.

Water quality trading has been proposed as a cost-effective approach for reducing nutrient loads through credit generation from agricultural or point source reductions sold to buyers facing costly options. We present a systematic approach to determine attenuation coefficients and their uncertainty. Using a process-based model, we determine attenuation with safety margins at many watersheds for total nitrogen (TN) and total phosphorus (TP) loads as they transport from point of load reduction to the credit buyer. TN and TP in-stream attenuation generally increases with decreasing mean river flow; smaller rivers in the modeled region of the Ohio River Basin had TN attenuation factors per km, including safety margins, of 0.19–1.6%, medium rivers of 0.14–1.2%, large rivers of 0.13–1.1%, and very large rivers of 0.04–0.42%. Attenuation in ditches transporting nutrients from farms to receiving rivers is 0.4%/km for TN, while for TP attenuation in ditches can be up to 2%/km. A 95 percentile safety margin of 30–40% for TN and 6–10% for TP, applied to the attenuation per km factors, was determined from the in-stream sensitivity of load reductions to watershed model parameters. For perspective, over 50 km a 1% per km factor would result in 50% attenuation = 2:1 trading ratio.

Greater scientific knowledge, changing societal values, and legislative mandates have emphasized the importance of implementing large‐scale flow experiments (FEs) downstream of dams. We provide the first global assessment of FEs to evaluate their success in advancing science and informing management decisions. Systematic review of 113 FEs across 20 countries revealed that clear articulation of experimental objectives, while not universally practiced, was crucial for achieving management outcomes and changing dam‐operating policies. Furthermore, changes to dam operations were three times less likely when FEs were conducted primarily for scientific purposes. Despite the recognized importance of riverine flow regimes, four‐fifths of FEs involved only discrete flow events. Over three‐quarters of FEs documented both abiotic and biotic outcomes, but only one‐third examined multiple taxonomic responses, thus limiting how FE results can inform holistic dam management. Future FEs will present new opportunities to advance scientifically credible water policies.

Experimental manipulations of streamflow have been used globally in recent decades to mitigate the impacts of dam operations on river systems. Rivers