Modeling \u3ci\u3eEscherichia coli\u3c/i\u3e in the Missouri River near Omaha, Nebraska, 2012–16

The city of Omaha, Nebraska, has a combined sewer system in some areas of the city. In Omaha, Nebr., a moderate amount of rainfall will lead to the combination of stormwater and untreated sewage or wastewater being discharged directly into the Missouri River and Papillion Creek and is called a combined sewer overflow (CSO) event. In 2009, the city of Omaha began the implementation of their Long Term Control Plan (LTCP) to mitigate the effects of CSOs on the Missouri River and Papillion Creek. As part of the LTCP, the city partnered with the U.S. Geological Survey (USGS) in 2012 to begin monitoring in the Missouri River. Since 2012, monthly discrete water-quality samples for many constituents have been collected from the Missouri River at four sites. At 3 of the 4 sites, water quality has been monitored continuously for selected constituents and physical properties. These discrete water-quality samples and continuous water-quality monitoring data (from July 2012 to 2020) have been collected to better understand the water quality of the Missouri River, how it is changing with time, how it changes upstream from the city of Omaha to downstream, and how it varies during base-flow conditions and during periods of runoff. The purpose of this report is to document the development of Escherichia coli (E. coli) concentration models for these four Missouri River sites. Analysis was completed using the first 5 years of data (through 2016) to determine if the current approach is sufficient to meet future analysis goals and to understand if proposed models such as Load Estimator (LOADEST) models will be able to represent water-quality changes in the Missouri River. Multiple linear regression models were developed to estimate E. coli concentration using LOADEST as implemented in the rloadest package in the R statistical software program. A set of explanatory variables, including streamflow and streamflow anomalies, precipitation, information about CSOs, and continuous water quality, were evaluated for potential inclusion in regression models. The best model at Missouri River at NP Dodge Park at Omaha, Nebr. (USGS station 412126095565201; hereafter “NP Dodge”) included basin explanatory variables of upstream antecedent precipitation index measured at Tekamah, Nebr.; decimal time; season; and turbidity. The best model at Missouri River at Freedom Park Omaha, Nebr. (USGS station 411636095535401; hereafter “Freedom Park”) included the same explanatory variables as the NP Dodge model with the addition of turbidity anomalies and flow anomalies. The best models at the two downstream sites (Missouri River near Council Bluffs, Iowa, USGS station 06610505 and Missouri River near La Platte, Nebr., USGS station 410333095530101) included the same explanatory variables as the Freedom Park model with the addition of local antecedent precipitation index as measured at Eppley Airport in Omaha, Nebr., and additional turbidity and flow anomalies. The final selected models were the best models given our modeling design constraint in which explanatory variables included in the model for the upstream site were included in the downstream models. Explanatory variables currently (2020) being collected and included in the selected models through 2016 explained 64–75 percent of the variability of E. coli concentration in the Missouri River. Explaining 64–75 percent of the variability might be considered low when working with physical constituents (total nitrogen or sediment), but with the natural variability of biological constituents such as E. coli, the uncertainty of E. coli laboratory measurements, and the added complexity of modeling in a large drainage basin with multiple sources, these results are adequate and indicate that the explanatory variables being collected and models such as LOADEST can represent water-quality changes in the Missouri River for E. coli concentration from 2012 to 2016

Hydrographic Surveys at Seven Chutes and Three Backwaters on the Missouri River in Nebraska, Iowa, and Missouri, 2011-13

The United States Geological Survey (USGS) cooperated with the United States Army Corps of Engineers (USACE), Omaha District, to complete hydrographic surveys of seven chutes and three backwaters on the Missouri River yearly during 2011–13. These chutes and backwaters were constructed by the USACE to increase the amount of available shallow water habitat (SWH) to support threatened and endangered species, as required by the amended “2000 Biological Opinion” on the operation of the Missouri River main-stem reservoir system. Chutes surveyed included Council chute, Plattsmouth chute, Tobacco chute, Upper Hamburg chute, Lower Hamburg chute, Kansas chute, and Deroin chute. Backwaters surveyed included Ponca backwater, Plattsmouth backwater, and Langdon backwater. Hydrographic data from these chute and backwater surveys will aid the USACE to assess the current (2011–13) amount of available SWH, the effects river flow have had on evolving morphology of the chutes and backwaters, and the functionality of the chute and backwater designs. Chutes and backwaters were surveyed from August through November 2011, June through November 2012, and May through October 2013. During the 2011 surveys, high water was present at all sites because of the major flooding on the Missouri River. The hydrographic survey data are published along with this report in comma-separated-values (csv) format with associated metadata.Hydrographic surveys included bathymetric and Real-Time Kinematic Global Navigation Satellite System surveys. Hydrographic data were collected along transects extending across the channel from top of bank to top of bank. Transect segments with water depths greater than 1 meter were surveyed using a single-beam echosounder to measure depth and a differentially corrected global positioning system to measure location. These depth soundings were converted to elevation using water-surface-elevation information collected with a Real-Time Kinematic Global Navigation Satellite System. Transect segments with water depths less than 1 meter were surveyed using Real-Time Kinematic Global Navigation Satellite Systems. Surveyed features included top of bank, toe of bank, edge of water, sand bars, and near-shore areas.Discharge was measured at chute survey sites, in both the main channel of the Missouri River upstream from the chute and the chute. Many chute entrances and control structures were damaged by floodwater during the 2011 Missouri River flood, allowing a larger percentage of the total Missouri River discharge to flow through the chute than originally intended in the chute design. Measured discharge split between the main channel and the chute at most chutes was consistent with effects of the 2011 Missouri River flood damages and a larger percent of the total Missouri River discharge was flowing through the chute than originally intended. The US Army Corps of Engineers repaired many of these chutes in 2012 and 2013, and the resulting hydraulic changes are reflected in the discharge splits

Modeling \u3ci\u3eEscherichia coli\u3c/i\u3e in the Missouri River near Omaha, Nebraska, 2012–16

The city of Omaha, Nebraska, has a combined sewer system in some areas of the city. In Omaha, Nebr., a moderate amount of rainfall will lead to the combination of stormwater and untreated sewage or wastewater being discharged directly into the Missouri River and Papillion Creek and is called a combined sewer overflow (CSO) event. In 2009, the city of Omaha began the implementation of their Long Term Control Plan (LTCP) to mitigate the effects of CSOs on the Missouri River and Papillion Creek. As part of the LTCP, the city partnered with the U.S. Geological Survey (USGS) in 2012 to begin monitoring in the Missouri River. Since 2012, monthly discrete water-quality samples for many constituents have been collected from the Missouri River at four sites. At 3 of the 4 sites, water quality has been monitored continuously for selected constituents and physical properties. These discrete water-quality samples and continuous water-quality monitoring data (from July 2012 to 2020) have been collected to better understand the water quality of the Missouri River, how it is changing with time, how it changes upstream from the city of Omaha to downstream, and how it varies during base-flow conditions and during periods of runoff. The purpose of this report is to document the development of Escherichia coli (E. coli) concentration models for these four Missouri River sites. Analysis was completed using the first 5 years of data (through 2016) to determine if the current approach is sufficient to meet future analysis goals and to understand if proposed models such as Load Estimator (LOADEST) models will be able to represent water-quality changes in the Missouri River. Multiple linear regression models were developed to estimate E. coli concentration using LOADEST as implemented in the rloadest package in the R statistical software program. A set of explanatory variables, including streamflow and streamflow anomalies, precipitation, information about CSOs, and continuous water quality, were evaluated for potential inclusion in regression models. The best model at Missouri River at NP Dodge Park at Omaha, Nebr. (USGS station 412126095565201; hereafter “NP Dodge”) included basin explanatory variables of upstream antecedent precipitation index measured at Tekamah, Nebr.; decimal time; season; and turbidity. The best model at Missouri River at Freedom Park Omaha, Nebr. (USGS station 411636095535401; hereafter “Freedom Park”) included the same explanatory variables as the NP Dodge model with the addition of turbidity anomalies and flow anomalies. The best models at the two downstream sites (Missouri River near Council Bluffs, Iowa, USGS station 06610505 and Missouri River near La Platte, Nebr., USGS station 410333095530101) included the same explanatory variables as the Freedom Park model with the addition of local antecedent precipitation index as measured at Eppley Airport in Omaha, Nebr., and additional turbidity and flow anomalies. The final selected models were the best models given our modeling design constraint in which explanatory variables included in the model for the upstream site were included in the downstream models. Explanatory variables currently (2020) being collected and included in the selected models through 2016 explained 64–75 percent of the variability of E. coli concentration in the Missouri River. Explaining 64–75 percent of the variability might be considered low when working with physical constituents (total nitrogen or sediment), but with the natural variability of biological constituents such as E. coli, the uncertainty of E. coli laboratory measurements, and the added complexity of modeling in a large drainage basin with multiple sources, these results are adequate and indicate that the explanatory variables being collected and models such as LOADEST can represent water-quality changes in the Missouri River for E. coli concentration from 2012 to 2016

Continuous Turbidity Data Used to Compute Constituent Concentrations in the South Loup River, Nebraska, 2017–18

The South Loup River in central Nebraska has been impaired by bacteria since at least 2004, which has resulted in the river not meeting its intended use as a recreational waterway. As part of a strategy for reducing the bacterial load in the river, the United States Geological Survey (USGS), in cooperation with the Lower Loup Natural Resources District, made continuous estimates of Escherichia coli (E. coli) and nutrient concentrations during seasonal monitoring at the South Loup River at Saint Michael, Nebraska, during 2017–18. Continuous turbidity data were collected from mid-April through October in 2017 and 2018 and were paired with 35 co-occurring discrete water samples that were analyzed for E. coli, nutrients, and suspended solids. Surrogate models relating the discrete concentrations to the continuous turbidity data were developed using ordinary-least-squares regression and were evaluated for model performance and uncertainty. Although the model assumptions were met for E. coli, the imprecision of the E. coli model was considerably higher than the other constituents, probably because of measurement imprecision and greater sensitivity to environmental factors. Once the models were developed, the turbidity data were used to predict continuous constituent concentrations and corresponding prediction intervals, which were made available online as part of the USGS National Water Information System database. It is expected that results from these models will provide stakeholders with an understanding of constituent concentrations during the 2017–18 monitoring period and the results will also provide a good reference point for any future comparisons

Hydrographic Surveys of Four Narrows within the Namakan Reservoir System, Voyageurs National Park, Minnesota, 2011

The United States Geological Survey (USGS) performed multibeam echosounder hydrographic surveys of four narrows in the Namakan reservoir system in August 2011, in cooperation with the International Joint Commission and Environment Canada. The data-collection effort was completed to provide updated and detailed hydrographic data to Environment Canada for inclusion in a Hydrologic Engineering Centers River Analysis System hydraulic model. The Namakan reservoir system is composed of Namakan, Kabetogama, Sand Point, Crane, and Little Vermilion Lakes. Water elevations in the Namakan reservoir system are regulated according to rule curves, or guidelines for water-level management based on the time of year, established by the International Joint Commission. Water levels are monitored by established gages on Crane Lake and the outlet of Namakan Lake at Kettle Falls, but water elevations throughout the system may deviate from these measured values by as much as 0.3 meters, according to lake managers and residents. Deviations from expected water elevations may be caused by between-lake constrictions (narrows). According to the 2000 Rule Curve Assessment Workgroup, hydrologic models of the reservoir system are needed to better understand the system and to evaluate the recent changes made to rule curves in 2000.Hydrographic surveys were performed using a RESON SeaBat™ 7125 multibeam echosounder system. Surveys were completed at Namakan Narrows, Harrison Narrows, King Williams Narrows, and Little Vermilion Narrows. Hydrographic survey data were processed using Caris HIPS™ and SIPS™ software that interpolated a combined uncertainty and bathymetric estimator (CUBE) surface. Quality of the survey results was evaluated in relation to standards set by the International Hydrographic Organization (IHO) for describing the uncertainty of hydrographic surveys. More than 90 percent of the surveyed areas at the four narrows have resulting bed elevations that meet the IHO “Special Order” quality. Survey datasets published in this report are formatted as text files of x-y-z coordinates and as CARIS Spatial ArchiveTM (CSARTM) files with corresponding metadata

Hydrographic surveys of the Missouri and Yellowstone Rivers at selected bridges and through Bismarck, North Dakota, during the 2011 flood

The United States Geological Survey (USGS), in cooperation with the North Dakota Department of Transportation and the North Dakota State Water Commission, completed hydrographic surveys at six Missouri River bridges and one Yellowstone River bridge during the 2011 flood of the Missouri River system. Bridges surveyed are located near the cities of Cartwright, Buford, Williston, Washburn, and Bismarck, N. Dak. The river in the vicinity of the bridges and the channel through the city of Bismarck, N. Dak., were surveyed. The hydrographic surveys were conducted using a high-resolution multibeam echosounder (MBES), the RESON SeaBatTM 7125, during June 6–9 and June 28–July 9, 2011. The surveyed area at each bridge site extended 820 feet upstream from the bridge to 820 feet downstream from the bridge. The surveyed reach through Bismarck consisted of 18 miles of the main channel wherever depth was sufficient. Results from these emergency surveys aided the North Dakota Department of Transportation in evaluating the structural integrity of the bridges during high-flow conditions. In addition, the sustained high flows made feasible the surveying of a large section of the normally shallow channel with the MBES.In general, results from sequential bridge surveys showed that as discharge increased between the first and second surveys at a given site, there was a general trend of channel scour. Locally, complex responses of scour in some areas and deposition in other areas of the channel were identified. Similarly, scour around bridge piers also showed complex responses to the increase in flow between the two surveys. Results for the survey area of the river channel through Bismarck show that, in general, scour occurred around river structures or where the river has tight bends and channel narrowing. The data collected during the surveys are provided electronically in two different file formats: comma delimited text and CARIS Spatial Archive™ (CSARTM) format

Saturated Thickness and Water in Storage in the High Plains Aquifer, 2009, and Water-level Changes and Changes in Water in Storage in the High Plains Aquifer, 1980 to 1995, 1995 to 2000, 2000 to 2005, and 2005 to 2009

The High Plains aquifer underlies about 112 million acres (about 175,000 square miles) in parts of eight States—Colorado, Kansas, Nebraska, New Mexico, Oklahoma, South Dakota, Texas, and Wyoming. Water levels declined in parts of the High Plains aquifer soon after the onset of substantial irrigation with groundwater (about 1950). This report presents the volume of saturated aquifer material and drainable water in storage in the High Plains aquifer in 2009; water-level changes in the High Plains aquifer from 1980 to 1995, 1995 to 2000, 2000 to 2005, and 2005 to 2009; and changes in the volume of drainable water in storage in the aquifer from 1980 to 1995, 1995 to 2000, 2000 to 2005, and 2005 to 2009. The volume data were calculated from raster files with a cell size of about 0.6 acres. The volume of water in storage in the High Plains aquifer in 2009 is estimated at about 3.0 billion acre-feet. Area-weighted, average water-level changes for the aquifer were declines of 2.0 feet from 1980 to 1995, 1.3 feet from 1995 to 2000, 2.8 feet from 2000 to 2005, and 1.0 foot from 2005 to 2009. Estimated changes in water in storage were declines of 36.0 million acre-feet from 1980 to 1995, 23.5 million acre-feet from 1995 to 2000, 46.7 million acre-feet from 2000 to 2005, and 18.3 million acre-feet from 2005 to 2009

Virtual Training Prepared for the Former Afghanistan Ministry of Energy and Water—Streamgaging, Fluvial Sediment Sampling, Bathymetry, and Streamflow and Sediment Modeling

The United States Geological Survey (USGS) created a virtual training series for the Afghanistan Ministry of Energy and Water (MEW), now known as the National Water Affairs Regulation Authority (NWARA), to provide critical hydrological training as an alternative to an in-person training. The USGS was scheduled to provide in-person surface-water training for NWARA during 2020; however, travel was halted because of the Coronavirus disease 2019 (COVID–19) pandemic. The virtual training consisted of prerecorded and live presentations that were scheduled during 4 weeks in August 2021. However, the training was halted after the second week due to the collapse of the Afghan Government. Fortunately, the prerecorded presentations and training materials were delivered before the trainings were halted, so they can be viewed or shared by the participants in the future. A benefit to having produced prerecorded trainings is that USGS can leverage or adapt the trainings for nongovernmental organizations (NGOs) involved in humanitarian water relief efforts in Afghanistan or can be used for other international training efforts