Berkeley Lab

May 2019 – Updates, virtual site visits, and more

As it’s been some time since my last email update with news, updates, and safety reminders, I wanted to get a condensed version out as we move into the busy field season.

  • Following what was a big snow year for Colorado and Crested Butte, we’ve had a relatively cold and wet May that has suppressed melt and runoff.  From a water perspective, this is very good news, with the exception of runoff forecasting, which has been hampered by the unseasonably cool weather.  From a field access perspective, however, it’s proving to be challenging.  We anticipate that the County Road out to Gothic will be open soon, although vehicular access won’t be possible past RMBL for the foreseeable future.  Those with field sites upstream of Gothic will need to be prepared to hike, ski, snowshoe, as warranted.
  • We successfully completed the first Airborne Snow Observatory (ASO) flight of the year during the so-called “Peak Snow Water Equivalent” period in early April.  For those who haven’t yet enjoyed the opportunity to dig snow pits tied to these ASO overflights, I wanted to provide two short “virtual site visits” depicting both pit digging and snow sampling.  I hope you enjoy and can envision yourselves helping out next year!  A second ASO flight is being used to evaluate regions of preferential snow retention within the Ohio Creek-East River-Taylor River study area; it’s planned for this Sunday-Monday (weather allowing).
  • Snow conditions at the higher elevations are still quite deep for this time of year.  Indeed, for those with field sites at higher elevations, access will be challenging for quite a while to come. Courtesy of Wendy and Tony Brown, photos of current conditions at the Lower Subalpine and Upper Subalpine field sites along the Washington Gulch elevation gradient will give you a virtual sense of what can be expected if you’re planning to head up soon.  For those on Kate Maher’s (Stanford) team, it might be worth looking at those from the Upper Subalpine site, as that’s the approach area for your Rock Creek study area.
  • Snow conditions at the two SNOTEL stations (Butte and Schofield) tell a similar story.  Below is a very nice figure prepared by Rosemary Carroll that depicts a variety of recent snow years for comparison with 2019 along with corresponding river discharge for the East River at Almont.  The aforementioned cool, wet weather in May has suppressed runoff of late; however, a lot of snow-bound water remains, and if we get a sustained warm up period, this melt could make for some very abrupt increases in discharge and flooding / over-banking along the river bottoms.
  • Related to these large increases in discharge, please use EXTREME caution when working along the river corridor.  Indeed, unless absolutely essential and your training permits working within the river during the rising and falling limbs of the hydrograph, please stay out of the rivers at this time.  Given her depth of knowledge and involvement with the stream gauging network, please reach out to Rosemary Carroll ( should you have specific questions about river conditions and whether access is (un)safe.
  • In April, we had an exciting field deployment of a novel electrochemical monitoring system performed as part of DOE’s Small Business Innovative Research (SBIR) Program.  The project, led by Dr. Don Nuzzio, is described more fully in this new “Meet the Scientist” video.  In brief, it uses a submerged electrode system to electrochemically quantify a variety of aqueous metals and compounds in various streams within the watershed.
  • Field teams from the SLAC SFA led by John Bargar are currently in the field.  Additionally, various members of our collaborating groups from Stanford, UMASS, Univ. Illinois – Chicago, and elsewhere are arriving daily and starting up the field work season.  Stay safe, warm, and dry out there folks!
  • With the incredible help of Chelsea Wilmer, Amanda Henderson, and Tony Brown, we’ve had tremendous success this year with the early snowmelt manipulation experiments.  Snowmelt tarps have been removed at both the Lower and Upper Montane sites with significant advancement of the first snow-free day at both locations.  The tarps are still deployed at the Lower Subalpine site with roughly 40-50 cm of snow still remaining underneath the tarped areas; un-tarped control areas have 100 cm remaining.  Tarps have yet to be deployed at the Upper Subalpine site given >240 cm of snow still remaining at that elevation.
  • As food for thought, I wanted to share a well-produced, short video describing ranching-related research activities pursued by the Archbold Biological Station (Florida) at their Buck Island Ranch   Along with my fellow RMBL Board members, I had the opportunity to visit Buck Island recently and I couldn’t have been more inspired by their studies investigating the many positive benefits of well managed land use on both hydrologic and biogeochemical processes.  Given the strong legacy of ranching and irrigated agriculture in the East River and Ohio Creek drainages, the Buck Island model might potentially represent an interesting one with which to engage local ranchers in our watershed.  For those with an interest in such topics or with faculty friends working in this space, I might suggest reaching out to myself and Ian Billick (, Executive Director of RMBL.
  • Lastly, I wanted to share a photo forwarded to me yesterday by Rosemary that highlights the beauty of the site this time of year.  It was taken by Connor Scalbom, who is doing some amazing photographic work in the valley.

Susan Hubbard Honored by Alameda County Women’s Hall of Fame

Susan Hubbard, Associate Laboratory Director for the Earth and Environmental Sciences Area, will be inducted into the Alameda County Women’s Hall of Fame, at an annual awards ceremony on March 30. Hubbard is being honored for her scientific contributions to key environmental challenges of our time, including the use of geophysical methods to quantify how watersheds and ecosystems are responding to changing conditions, and implications for water and biogeochemical cycles.

Susan Hubbard joins 13 other local women who represent the region’s rich diversity and a remarkable range of achievements made working to address issues such as environmental sustainability; and racial, income, and healthcare inequality; and to strengthen access to arts education and athletics programs for girls and young women.

Replicating subsurface processes in the laboratory

2.0 m tall laboratory sediment column and example measurements. a. instrument distribution, b. column clad with heat exchangers, c. column with insulation sleeve, d. seasonal field temperature profiles replicated in column, e. seasonal CO2 profiles from laboratory column.

Fluid flows with temperatures that are not constant are known as non-isothermal. Although changing thermal and hydrological conditions control rates of sediment biogeochemical processes in the Earth’s subsurface, these conditions are difficult to simulate in the laboratory. In this study, a novel 2 m tall column system to control time- and depth-dependent temperature profiles and water saturation was developed, which is needed to more accurately reproduce subsurface processes in the laboratory.

Temperature and moisture profiles in sediments are highly variable, and control biogeochemical processes, yet have not previously been reproduced in the laboratory. This study established field temperature and moisture profiles in a laboratory column system, and showed the importance of microbial respiration below the plant root zone by measuring CO2 production within the sediment column.


Transport between the soil surface and groundwater is commonly mediated through deeper portions of variably saturated sediments and the capillary fringe, where variations in temperature and water saturation strongly influence biogeochemical processes. Temperature control is particularly important because room temperature is not representative of most soil and sediment environments. The authors described and tested a novel sediment column design that allows laboratory simulation of thermal and hydrologic conditions found in many field settings. The 2.0 m tall column was capable of replicating temperatures varying from 3 to 22 ˚C, encompassing the full range of seasonal temperature variation observed in the deep, variably saturated sediments and capillary fringe of a semi-arid floodplain in western Colorado, United States. The water table was varied within the lower 0.8 m section of the column, while profiles of water content and matric (capillary) pressure were measured. CO2 collected from depth-distributed gas samplers under representative seasonal conditions reflected the influences of temperature and water-table depth on microbial respiration. Thus, realistic subsurface biogeochemical dynamics can be simulated in the laboratory through establishing column profiles that more accurately represent seasonal thermal and hydrologic conditions.


Tokunaga, T.K., Y. Kim, J. Wan, M. Bill, M. Conrad, and W. Dong, “Method for Controlling Temperature Profiles and Water Table Depths in Laboratory Sediment Columns. Vadose Zone Journal 17,180085 (2018). [DOI: 10.2136/vzj2018.04.0085]

October 2018 – Quick update and hunting season reminder

I wanted to send along a short “virtual site visit” presenting the recent (and ongoing) shale drilling activity at East River. This visit will find you on the Pumphouse lower montane hillslope as we core a 70m deep borehole designed to capture hydrogeochemical processes much deeper than we’ve done so to date.

In general the coring has gone well, however, the weather gods have not been cooperative, as conditions along the steep access road have been challenging. We paused drilling for safety reasons tied to the recent ~30cm of snowfall, and we will be resuming coring at two locations close to Gothic designed to collect samples from regions of the Mancos shale more heavily altered by igneous intrusives. A final update will follow once we finish up that work toward the end of this coming week.

During the drilling activity, we’ve had the pleasure of welcoming Lee Liberty of Boise State University to the watershed. Lee is a newly funded DOE University PI, and he and his team are collecting seismic reflection data along many of the roads within our study area using a novel tow-along seismic streamer. We look forward to having Lee update us on his project and findings during a future Watershed Science Community call.

Important Health and Safety Reminders

The first rifle hunting season starts today Saturday Oct. 13 and runs through Oct. 17th; the second rifle season is Oct. 20-28. Please wear an orange vest, hat or jacket for visibility and safety. Like other personal protective equipment, the costs of these vests, hats, etc. are reimbursable. Please stop by the local hardware store, Walmart, or sporting goods store to purchase these supplies if you will be in the field during hunting season.

Related to this, I wanted to emphasize the importance of suitable field gear. We recently had an incident where one of our employees fell while trying to cross the East River near the Rustlers Gulch access point. As many know, this crossing has become challenging over the past year due to a large beaver dam immediately downstream of the crossing. Multiple cars have flooded their engines trying to cross earlier in the year, as the water line was above the engine air intake. As a result, many folks are crossing the river by foot upstream using logs and rocks to avoid getting their feet a bit wet. Such crossings can be challenging — the proverbial falling off a log. For safety reasons, such crossings should be made using appropriate footwear, such as hip boots, waders or water shoes, in order to minimize risk associated with walking the tightrope so to speak. Please don’t risk an injury just trying to keep your toes dry. As with the orange vests and hats, the costs for proper field footwear are reimbursable expenses.

Sustainable Remediation of Complex Environmental Systems: Key Recent Technical Advances

Simulated uranium plume (concentration>1×10-6mol/L) in 3D at the Savannah River Site F-Area in 2050. The sky-blue region is the low permeable Tan Clay Zone, which separates the upper and lower aquifers.

This book chapter provides an overview of the key recent scientific advances to support sustainable remediation in complex geological systems demonstrated at the Savannah River Site F-Area, including site characterization techniques, hydrological and geochemical model developments and numerical simulations.

We have developed various subsurface characterization and modeling technologies to improve the predictive understanding of the groundwater contaminant plumes in complex geological systems. The technologies have been demonstrated at the Department of Energy’s Savannah River Site.


Groundwater remediation has been evolved recently with increased focus on sustainable approaches such as in situ treatments and natural attenuation. However, leaving contaminants in subsurface requires the increased burden of proof to show that plumes are stable and residual contaminants do not pose a significant health risk. At the Department of Energy’s Savannah River Site, we have developed and demonstrated various characterization and modeling technologies to provide the predictive understanding of the contaminant plume migration, including (1) a multiscale data integration method to integrate surface seismic and borehole datasets that have different resolution and spatial coverage, (2) a novel surface complexation model to describe pH-dependent uranium sorption behavior based on readily available datasets, and (3) a reactive transport modeling and uncertainty quantification framework to predict the future uranium plume behavior and to identify key parameters on the future uranium concentration. These technologies are expected to transform groundwater remediation at many other sites.


Wainwright, H. M.; Arora, B.; Faybishenko, B.; Molins, S.; Hubbard, S. S.; Lipnikov, K.; Moulton, D.; Flach, G.; Eddy-Dilek, C.; Denham, M. (2018), Sustainable Remediation in Complex Geologic Systems, The heaviest metals: Science and technology in Actinides and beyond.

Bhavna Arora speaks with News Deeply about the consequences of drought on Colorado

Bhavna Arora (right) and former intern Madison Burrus discuss the computer simulations they are creating using data about river discharge, precipitation, and snowpack collected from the East River catchment site near Crested Butte, CO. (Credit: Marilyn Chung/Berkeley Lab)

SFA researcher Bhavna Arora was interviewed on Water Deeply regarding how declining snowpack is altering water quality in the Colorado River.

A more comprehensive interview and story were conducted by the Berkley Lab News Center, where Bhavna explains how drought and other extremes impact water pollution. Read more »

Vadose Zone Journal Special Issue features Watershed Function SFA Overview

An overview of the Watershed function SFA and the associated East River Watershed was published in in the Vadose Zone Journal “Special Section: Hydrological Observatories”. The paper describes several recently developed approaches to interrogate, monitor and simulate transient watershed partitioning and biogeochemical responses – from genome to watershed spatial scales and from episodic to decadal timescales.

View the full paper (open access) here.

Geochemical Exports to River from the Intra-Meander Hyporheic Zone under Transient Hydrologic Conditions at East River

Figure 1: Spatial distributions of dissolved geochemical species in groundwater in the meander C.

Hyporheic exchange within the intra-meander region results in the interaction of nutrient-rich groundwater and oxygen-rich river water, which leads to the formation of distinct redox gradients. These redox gradients can significantly impact the export of metals and nutrients at the local, reach, and watershed scales. Further, transient hydrologic conditions, such as groundwater flow dynamics, river-stage fluctuations, and rainfall/snowmelt events, can impact redox processes in the hyporheic zone and ultimately the geochemical exports to the river thereby affecting river water quality. Here we have used high-resolution hydrodynamic assessments of the hyporheic zone combined with detailed pore-water sampling to focus on the hyporheic exchange at the meander scale for the purpose of quantifying the subsurface exports from a single meander to the river under transient hydrological conditions.

This study is a first of its kind that examines the influence of transient hydrological conditions on the hyporheic biogeochemistry using field observations. Simulation results demonstrated that intra-meander hyporheic zones display distinct anoxic and suboxic regions, suboxic regions being localized along sides of the meander bend. Permeability within the meander has a more significant impact on biogeochemical zonation compared to the reaction pathways for transient hydrologic conditions. Here we have also demonstrated the outsized implications of micro-topographic features such as gullies on redox processes using the high-resolution LiDar data.

Figure 2. Net cumulative geochemical export of TIC, DOC, and iron(II) from a single meander. River-stage is shown in green on the right y-axis, whereas the net export is shown in golden color on the left y-axis.


Hyporheic zones perform important ecological functions by linking terrestrial and aquatic systems within watersheds. Hyporheic zones can act as a source or sink for various metals and nutrients. Transient hydrologic conditions alter redox conditions within an intra-meander hyporheic zone thus affecting the behavior of redox-sensitive species. Here we investigated how transient hydrological conditions control the lateral redox zonation within an intra-meander region of the East River and examined the contribution of a single meander on subsurface exports of carbon, iron, and other geochemical species to the river. The simulation results demonstrated that the reductive potential of the lateral redox zonation was controlled by groundwater velocities resulting from river-stage fluctuations, with low-water conditions promoting reducing conditions. The sensitivity analysis results showed that permeability had a more significant impact on biogeochemical zonation compared to the reaction pathways under transient hydrologic conditions. The simulation results further indicated that the meander acted as a sink for organic and inorganic carbon as well as iron during the extended baseflow and high-water conditions; however, these geochemical species were released into the river during the falling limb of the hydrograph. This study demonstrates the importance of including hydrologic transients, using a modern reactive transport approach, to quantify exports within the intra-meander hyporheic zone at the riverine scale.


Dwivedi, D., C.I. Steefel, B. Arora, M. Newcomer, J.D. Moulton, B. Dafflon, B. Faybishenko, P. Fox, P. Nico, N. Spycher, R. Carroll, and K.H. Williams (2018), Geochemical Exports to River from the Intra-Meander Hyporheic Zone under Transient Hydrologic Conditions: East River Mountainous Watershed, Colorado, Water Resources Research, 10.1029/2018WR023377.

First Watershed Science Collaboration Workshop takes place Sep 23-25, 2018 in Crested Butte, CO

The workshop began with a guided tour of the East River watershed.

Attendees pose briefly for a group photo.

Attendees included microbial and plant ecologists, hydrologists, geochemists, geologists, geophysicists, remote and snow sensing experts, data and computational scientists and resource managers. Read more »

Using strontium isotopes to evaluate how local topography affects groundwater recharge

Figure 1. 87Sr/86Sr vs 1/[Sr] showing the mixing relationships between vadose zone porewater and groundwater. Blue line shows the mixing model of vadose zone water with upgradient groundwater with bold numbers representing the percentage of vadose zone water in the local aquifer.

A key component of understanding the connection between groundwater quality and the vadose zone (the water unsaturated region above the water table) is the movement of water from the surface to the aquifer (recharge). Measurements of the natural isotopic composition of Sr were used to assess the effect of local topography on groundwater recharge across a semi-dry riparian floodplain in the Upper Colorado River Basin.

This work demonstrates the use of 87Sr/86Sr (Sr isotopes) to measure groundwater recharge through analysis of porewater and groundwater samples from the vadose zone. The study resulted in an understanding how the microtopography of the Rifle Site affects the hyper-local variation in the downward movement of vadose-zone porewater that may carry nutrients and contaminants to groundwater.

Figure 2. “Heat” map of the percentage contribution of vadose water to the Rifle floodplain aquifer based on the Sr isotopic mixing model.


Over time, loose sand, clay, silt, gravel or similar unconsolidated, or “alluvial” material is deposited by water into alluvial aquifers. Recharge of alluvial aquifers is a key component in understanding the interaction between floodplain vadose zone biogeochemistry and groundwater quality. The Rifle Site (a former U-mill tailings site) adjacent to the Colorado River is a well-established field laboratory that has been used for over a decade for the study of biogeochemical processes in the vadose zone and aquifer. This site is exemplary of both a riparian floodplain in a semiarid region and a post-remediation U-tailings site. The authors use Sr isotopic data for groundwater and vadose zone porewater samples to build a mixing model for the fractional contribution of vadose zone porewater (i.e. recharge) to the aquifer and to assess its distribution across the site. The vadose zone porewater contribution to the aquifer ranged systematically from 0% to 38% and appears to be controlled largely by the microtopography of the site. The area-weighted average contribution across the site was 8%, corresponding to a net recharge of 7.5 cm. Given a groundwater transport time across the site of ~1.5 to 3 years, this translates to a recharge rate between 5 and 2.5 cm/yr, and with the average precipitation to the site, implies a loss from the vadose zone due to evapotranspiration of 83% to 92%.


Christensen, J. N., et al. (2018), Using strontium isotopes to evaluate the spatial variation of groundwater recharge, Sci Total Environ, 637-638, 672-685, DOI: 10.1016/j.scitotenv.2018.05.019.