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United States Department of Agriculture

Agricultural Research Service

Choptank River, Maryland
An ARS Benchmark Research Watershed

Environmental Impacts
Management Practices
Research Objectives
Selected References
Collaborators and cooperating Agencies and Groups


The Choptank River is an estuary and tributary of the Chesapeake Bay. It is located in the coastal plain on the Delmarva Peninsula in the Mid-Atlantic Region of the United States. The Choptank basin has an area of 2057 km2 (794 sq. mi.). Land use within the watershed is classified as 52% agriculture, 26% forested, and 5% developed. Agricultural production is centered on the poultry industry with large-scale corn, soybean, and small grains production. The river originates in Kent County, Delaware and flows southwest. The lower estuarine segment of the Choptank River is a tidal embayment, and its ecosystem status is reflective of the greater Chesapeake Bay. The single U.S. Geological Survey (USGS) monitoring station on the main stem of the Choptank River near Greensboro, Maryland (USGS station #014910000) roughly marks the transition to non-tidal reaches for the main branch and above, draining 14% of the watershed. Drainage from the Tuckahoe Creek sub-basin enters the main stem of the Choptank in the tidal region. The Tuckahoe Creek sub-basin is 690 km2 (266 sq. mi.) and represents 34% of the Choptank watershed.

Ator et al. (2005) classified a large section of the Delmarva Peninsula including most of the Choptank River watershed as belonging to the Middle Coastal Plain. This region was defined by the superposition of upper-delta-plain sands and gravel that overlay marine inner shelf sands. The drainage network has not been fully developed with original flat upland surface being only partly dissected by streams. In the absence of underlying restrictive layers, good drainage is expected in the region because of moderate topographic relief and underlying sands and gravel with good permeability. Streams and groundwater in this region are considered to be highly susceptible to contamination by chemicals applied to the landscape. Extensive nitrate contamination in groundwater has been documented within this region (Fisher et al. 2006). Although the shallow groundwater generally contains high concentrations of contaminants in the areas of application, concentrations in the streams are more variable because base-flows generally represent a mixture of groundwater from the entire watershed which includes areas with minimal chemical application.

Considerable hydrogeological variability is found within the Choptank River watershed. A detailed classification of hydrogeomorphic properties for the Costal Plain was put forward by Phillips et al. (1993) to describe variation in hydrologic conditions. The lowland sub-regions cover the coastal margins of the watershed. The hydrology in these regions is heavily influenced by tides. The fine-grained lowland (FGL) sub-regions have surficial sediments composed of silts, sands and organic muds that were deposited on the landscape with changes in sea level. The near-surface sediments in this region have low permeability. The poorly-drained lowland (PDL) region consists of coarser grained sediments (mostly sands) than those found in FGL.

The upland areas of the Choptank watershed can be divided into well-drained (WDU) and poorly-drained (PDU) sub-regions. The WDU sub-regions are characterized by well-drained land areas on topographic highs and poorly-drained soil on floodplains in stream valleys. Streams are more highly incised with the topography being relatively flat to gently rolling within this hydrogeomorphic sub-region. Land use consists mostly of agricultural crop production on upland portions of watersheds with wooded areas found along the narrow riparian zones associated with incised streams. The typical groundwater flow paths in this hydrogeomorpholgy range from one to several kilometers (Lowrance et al. 1997).

The PDU sub-regions are characterized by a mixture of poorly-drained forests and moderately well-drained and well-drained agricultural land (Shedlock et al 1993). Streams are small and slow running in these poorly-drained uplands with shallow incision of valleys with low gradients. Riparian zones in the sub-region are forested and usually contain wetlands. This region contains many seasonally inundated depressions under forest vegetation. An extensive ditch drainage network has been developed for large parts of this region allowing conversion of wetlands to cropland agriculture. The typical groundwater flow paths in this hydrogeomorpholgy range from 100 meters to about one kilometer (Lowrance et al. 1997).

The major soil types found under cropland production in the Choptank watershed are typified by the Othello soil series (fine-silty, mixed, active, mesic typic endoaquults) and the Mattapex soil series (fine-silty, mixed, active, mesic aquic hapludults). These soils formed from parent material consisting of silty eolin sediments underlain by coarser marine, eolin, fluvial, or alluvial sediments. Othello soils are poorly-drained with moderately slow permeability and Mattapex soils are moderately well-drained with moderate or moderately slow permeability.

Environmental Impacts

1. Water Quality: Nutrient, sediment, and bacterial contamination are critical water quality problems. Pesticides and other organic contaminants are also a concern.

2. Soil Quality: Soil quality concerns center on maintenance of soil tilth by preserving and sequestering carbon in soils.

3. Air Quality: Ammonia and odorous emissions from activities connected with poultry production and the associated challenges that arise from increasingly complex urban-rural interface are air quality concerns within the watershed.

4. Loss of wetlands and wildlife habitat: Historical loss of wetlands in the Upper Choptank River sub-watershed is large compared to similar Maryland watersheds.

5. Ecosystem health of the Chesapeake Bay: Low dissolved oxygen, low water clarity, health of submerged aquatic vegetation, and populations of oysters, clams, and blue crabs dominate the list of ecosystem health concerns.

Management Practices

1. Cover crops (340)
2. Crop residue management (329A and 329B)
3. Nutrient management (590)
4. Ditch drainage management (554)
5. Field borders (386)
6. Filter strips (393)
7. Riparian forest buffers (391)
8. Streambank and shoreline protection (580)
9. Tree and shrub establishment (612)
10. Wetland management and restoration (657)

Research Objectives

1. Evaluate the effectiveness of conservation practices in the Mid-Atlantic region on a watershed scale.
2. Contribute to the efforts to improve and protect water quality in the Chesapeake Bay.
3. Build upon the strong partnerships established in this project between scientists, conservation specialists, extension agents, and farmers, which have resulted in a framework to examine the most promising and widely-used conservation practices in the region.
4. Collect improved information on the processes and mechanisms influencing the effectiveness of conservation practices to enhance existing water quality models.
5. Transfer project results to conservation specialists, extension agents, and farmers' groups to increase the effectiveness of their programs.



Available long term monitoring datasets. As part of the Chesapeake Bay watershed, the Choptank River is included in a number of on-going monitoring efforts conducted by several state and federal agencies. A historical water quality dataset of monthly nutrient and suspended solids concentration and water discharge, which began in 1975, is available from a station in the Upper Choptank River as part of the USGS Chesapeake Bay River Inputs Monitoring Program ( The Choptank River watershed was also included in a USGS National Water Quality Assessment Program study of the Delmarva Peninsula from 1999 to 2001 (Denver et al. 2004). As part of the larger Chesapeake Bay Water Quality Monitoring Program, MD-DNR and University of Maryland Horn Point Laboratory have carried out monthly or bimonthly water quality monitoring at four stations within main stem of the Choptank River since 1984 ( Samples have been characterized for temperature, pH, salinity, dissolved oxygen, total suspended solids, Secchi depth, nutrients and chlorophyll. In addition, there are three continuous water quality monitoring stations maintained by University of Maryland and MD-DNR along the main stem providing dissolved oxygen, salinity, water temperature, pH, and turbidity.

The Choptank River is also covered by the NOAA National Status and Trends, Mussel Watch Program. A large number of organic and inorganic contaminants have been measured in oysters from one station in the lower estuary since 1986 ( A National Atmospheric Deposition Program (NADP) monitoring station exists adjacent to the Choptank basin at the Wye Research and Education Center (NADP station MD13, where weekly, composite rainfall quantity and chemistry have been monitored continuously since 1982. On a smaller scale, a long term monitoring project of nutrients, sediment, and discharge was carried out within one of our study sub-watersheds from 1990 to 1995 (Primrose et al. 1997).

Current water quality monitoring. Water quality monitoring efforts as part of the Choptank River CEAP have focused on baseflow grab samples collected at the outflow of the 15 sub-watersheds. Each sub-watershed has been characterized with respect to land use, percent hydric soils, and the location of CREP/CRP buffers. Monthly baseflow samples have been collected at these stations since January of 2003. These sub-watersheds were selected as part of an earlier University of Maryland project on the effectiveness of riparian buffers in protecting water quality (Sutton 2005); additional sampling was also conducted in 1986-1987 (Norton and Fisher 2000). Monthly water quality measurements are available for 2003 to the present. Water samples are characterized for ammonium, nitrate, nitrite, total N, phosphate, total P, and total suspended particle concentrations. Beginning in June 2005, a suite of currently- and historically-used pesticides and their degradation products were added to the contaminants monitored. Each station is also continuously monitored for stage height and temperature using a sensor with internal datalogger anchored to the stream bead (Solinst Canada, Georgetown, Ontario, Canada). A stage-discharge relationship has been developed for each site using manual velocity/area measurements under baseflow conditions and an Acoustic Doppler Current Profiler (StreamPro ADCP, RD Instruments San Diego CA) for storm flows. Selected storm flow events have been characterized hourly for 48 hours on 6 streams using autosamplers (ISCO, Lincoln NE).

In a parallel effort as part of a NOAA-funded study, additional contaminants were measured on a quarterly basis at the 15 sub-watershed sites along with 7 stations in the lower estuary. In,2005 arsenic, copper, selected veterinary antibiotics, and hormones, were measured along with nutrients, agricultural pesticides and their degradation products, and sediments. Additional sampling at the 7 estuary sites has continued since 2006, on a near monthly basis, for nutrients, pesticides and their degradation products, and sediments only.

Water quality data and other pertinent data sets will be submitted to the U.S. Department of Agriculture, Agricultural Research Service, Sustaining the Earth's Watersheds – Agricultural Research Data System (STEWARDS) Database for comparison with other participating watersheds in the CEAP.

Remote sensing for cover crop nutrient uptake assessment. A collaborative effort between USDA-ARS and MDA has led to an innovative approach to evaluate the effectiveness of winter cover crops for sequestration of the soil nitrogen that is residual from the previous growing season. This approach uses remote sensing data, field sampling, and cost share program enrollment data (field locations, planting date, method, species, previous crop) provided by farmers to derive real-time estimates of cover crop biomass production and nitrogen. For this approach, 4 wavelength bands images with 10 m resolution are acquired by SPOT Earth observation satellite for the area of interest within the Choptank River watershed. From the analysis of the remotely-sensed data, a vegetative index (Normalized Difference Vegetative Index, (NDVI)) measurement is calculated which can be correlated to the on-farm biomass and nitrogen uptake measurements using a subset of fields within the program. These derived relationships can then be extrapolated to the entire population of cost-share program fields within the image for estimating biomass production and nutrient uptake. Use of this efficient monitoring technology for cover crops is expected to allow program and watershed managers to optimize implementation of this important best management practice at watershed and regional scales.

Satellite-based radar for forested wetland detection and characterization. Wetlands provide beneficial ecological services, including water quality improvements. Hydrology (i.e., flooding and soil moisture) controls wetland function and must be better understood to predict the delivery of beneficial services and to improve water quality management. Maps that delineate patterns of wetland hydrology have been difficult to produce especially for forested wetlands, which comprise over half of all US wetlands and the vast majority of wetlands at the Choptank River watershed. Indeed, forested wetlands are one of the most difficult types of wetlands to map using optical imagery, such as aerial photographs and Landsat, and ground-based approaches are resource prohibitive over the large areas often necessary for watershed management. In addition, existing wetland maps, such as the U.S. Fish and Wildlife Service National Wetland Inventory, are difficult to update and represent conditions at one point in time. New methods must be developed to obtain a more complete picture of these dynamic ecosystems and to improve estimates of water quality.

Satellite-based radar sensors have the unique capability to monitor changes in the status of the key hydrologic characteristics of wetlands throughout the year and with greater frequency, in part due to the ability of radars to collect images regardless of cloud cover, day or night. Not being restricted by clouds is especially important when collecting data during rainy periods when wetlands are often easier to discriminate. The sensitivity of radar energy to water and its ability to penetrate forest canopies makes radar sensors ideal for the detection of hydrologic patterns in forested wetlands. Although the capability of radar images for wetland research is promising, the technology is relatively new compared to other types of sensors and further research is required to develop this capability. In the future, radar-derived maps of hydrology will be used to estimate ecosystem services (e.g., water quality improvement via denitrification) in wetlands throughout the Choptank River Watershed including those receiving agricultural runoff.

Nitrogen and oxygen isotopes as tools to assess denitrification. Assessing the role of denitrification in the fate of agricultural nitrogen at landscape and watershed scales has been an intractable problem, but such assessments are needed to measure more accurately the effectiveness of BMPs, such as riparian buffers for streams and controlled drainage management of ditches, to mitigate nutrient pollution. The isotopic composition of nitrogen and oxygen in nitrate can signal nutrient source and/or extent of biogeochemical processing of the nitrate pool by denitrifiers within ecosystems (Mayer et al. 2002). Denitrification will cause enrichment of 15N and 18O in nitrate with an accompanying decrease in nitrate concentrations. The amount of denitrification can be calculated from the changes in isotope abundances according to known Rayleigh fractionation relationships (Lindsey et al. 2003). Separation of the different isotopic signals may be challenging, but in cases where sources such as commercial fertilizers are well characterized, the biogeochemical signal can be differentiated.

For groundwater samples, dissolved gas analysis (N2 and Ar) was used to detect the excess dissolved N2 resulting from denitrification (Bohlke, 2002; Mookherji et al. 2003) which was then correlated with the isotopic signatures in the nitrate pool. These combined measurements for groundwater can also provide calibration for the isotopic signatures for nitrate found in ditches and streams which integrates denitrification measurements to the scale of drainage.

These landscape-scale assessments of denitrification based on isotopic data have proved useful for assessing effects of land use on nitrogen export. Analysis of stream water from 13 sub-watersheds in the Choptank River watershed showed a strong linear relationship between nitrate concentration and land area under crop production. The residuals between measured nitrate concentrations and predicted concentrations (from regression line in plot 7A) were roughly correlated with enrichment of the 18O isotope (δ18O). Therefore, the process of denitrification results in enrichment of the heavier 18O isotope in the nitrate remaining in the stream. These preliminary findings suggest this approach may be valuable in assessing denitrification processes across a landscape scale.

Water quality watershed modeling. A critical component of CEAP is the watershed scale assessment of conservation practices as facilitated by application of water quality models. In recent years, a significant number of state and federal incentive programs have been implemented for water quality improvement in the Choptank River watershed, but environmental benefits from these programs have never been quantified at watershed scales. Two of the most widely-used USDA watershed-scale models, Soil and Water Assessment Tool (SWAT) and Annualized Agricultural Non-Point Source (AnnAGNPS) are being utilized in the present study to quantify the environmental benefits from the implementation of BMPs, such as winter cover crops and riparian buffers. Efforts are underway to link the Riparian Ecosystem Management Model (REMM) to either AnnAGNPS or SWAT in order to better simulate riparian buffer efficiency.

Although there are some differences in model input requirements between AnnAGNPS and SWAT, the common inputs include digital elevation model (DEM), land cover, soil types, weather data, and agronomic management information. To date, the standard USGS 30 m DEM has been the base for all derived topographic data for watershed delineation and stream flow networks. The low relief of the watershed makes the 30 m DEM marginal for this purpose. In 2007, very high resolution LIDAR DEM data (15 cm vertical accuracy) will become available for the entire Choptank watershed through the MD-DNR ( which will permit the establishment of more accurate watershed boundaries and flow path delineations within low relief topographies. Weather datasets have also provided a significant challenge in modeling efforts. Summer storms lead to highly variable precipitation rates across the study region. The primary dataset utilized in the models was collected in Easton, MD, a few kilometers outside the watershed. This variability can lead to significant errors in flow predictions, especially when working in small watersheds.

Five years (1991-1995) of detailed observed flow and water quality data collected from the German Branch sub-basin (Primrose et al., 1997) were used to provide baseline calibration and validation for the two models (Sadeghi et al. 2007). Results indicate that both models performed adequately for simulating hydrologic conditions; however, AnnAGNPS predicted lower than observed nitrate loads during the summer months (Sadeghi et al. 2007). A comparison of SWAT and AnnAGNPS simulations of random implementation of cover crops within the German Branch sub-watershed showed that both models predicted only slight reduction in nitrate loading resulting from 40% implementation but greater reduction with 70% implementation.

The SWAT model, because of its special hydrologic response unit (HRU) formation, can be used to identify the pollutant loads associated with specific management practice for a given soil type and land use combination. A SWAT simulation of the German Branch comparing random versus targeted implementation of cover crops in HRUs with the greatest nitrate loads (data not shown) predicted marked improvement in load reduction with the targeted implementation. However, spatial information on pollutant loads are not provided using SWAT, whereas the AnnAGNPS model, because of its unique cell-based structure, is better able to identify the precise spatial location for specific pollutant loads within a watershed. At present, limitations associated with input datasets allow for only relative comparisons of model output results for BMP implementation scenarios.

While current modeling efforts have been limited to one sub-watershed, future efforts will be expanded to include the other study sub-watersheds and eventually the entire Choptank River watershed. New research initiatives as part of a U.S. EPA-funded Targeted Watersheds project are to develop a watershed BMP planning tool for the entire Choptank River watershed including the tidal portions of the estuary. Improved infrastructure for weather data collection in the study areas will be required for more accurate model outputs. In addition, continued interaction with federal, state and county action agencies will be needed to obtain information on BMP implementation and changes in nutrient management practices.


Selected References

Ator, S.W., Denver, J.M., Krantz, D.E., Newell, W.L. and S.K. Martucci. 2005. A surficial hydrogeologic framework for the Mid-Atlantic coastal plain. Professional Paper 1680. Reston, VA: U.S. Geological Survey. .

Bohlke, J. K. 2002. Groundwater recharge and agricultural contamination. Hydrogeology Journal 10:153-179.

Denver, J.M., Ator, S.W., Debrewer, L.M., Ferrari, M.J., Barbaro, J.R., Hancock, T.C., Brayton, M.J., and M.R. Nardi. 2004. Water Quality in the Delmarva Peninsula, Delaware, Maryland, and Virginia, 1999–2001. Circular 1228. Reston VA: U.S. Geological Survey.

Fisher, T.R., Hagy, J.D., Boynton, W.R., Lee, K.-Y., and M.R. Williams. 2006. Cultural eutrophication in the Choptank and Patuxent estuaries of Chesapeake Bay. Limnology and Oceanography 51:435–447.

Lindsey, B.D., Phillips, S.W., Donnelly, C.A., Speiran, G.K., Plummer, L.N., Bohlke, J.K., Focazio, M.J., Burton, W.C., and E. Busenberg. 2003. Residence times and nitrate transport in ground water discharging to streams in the Chesapeake Bay watershed. U.S. Geological Survey Water Resources Investigations Report 03-4035. New Cumberland, PA: U.S. Geological Survey.

Lowrance, R., Altier, L.S., Newbold, J.D., Schnabel, R.R., Groffman, P.M., Denver, J.M., Correll, D.L., Gilliam, J.W., Robinson, J.L., Brinsfield, R.B., Lucas, W., and A.H. Todd. 1997. Water quality functions of riparian forest buffers in Chesapeake Bay watersheds. Environmental Management 21:687-712.

Mayer, B., E., Boyer, W., Goodale, C., Jaworski, N. A., Van Breemen, N., Howarth, R. W., Seitzinger, S., Billen, G., Lajtha, K., Nadelhoffer, K., Van Dam, D., Heting, L. J., Nosal, M., and K Paustian. 2002. Sources of nitrate in rivers draining sixteen watersheds in the northeastern U.S.: Isotopic constraints. Biogeochemistry 57/58:171-197.

Mookherji, S., McCarty, G.W., and J.T. Angier. 2003. Dissolved gas analysis for assessing the fate of nitrate in wetlands. Journal of the American Water Resources Association 39:381-387.

Norton, M.G. and T R. Fisher. 2000. The effects of forest on stream water quality in two coastal plain watersheds of the Chesapeake Bay. Ecological Engineering 14:337-362

Phillips P.J., J.M. Denver, R.J. Shedlock, and P.A. Hamilton. 1993. Effect of forested wetlands on nitrate concentrations in ground water and surface water on the Delmarva Peninsula. Weltands 13:75-83.

Primrose J.L., C.J. Millard, J.L. McCoy, M.G. Dobson, P.E. Sturm, S.E. Bowen and R.J. Windschitl. 1997. German branch. Targeted watershed project-biotic and water quality monitoring evaluation report 1990–1995. Annapolis, MD: Chesapeake and Coastal Watershed Service, Watershed Restoration Division, Maryland Department of Natural Resources, CCWS-WRD-MN-97-03.

Sadeghi, A., K. Yoon, C. Graff, G. McCarty, L. McConnell, A. Shirmohammadi, D. Hively, K. Sefton. 2007. Assessing the Performance of SWAT and AnnAGNPS Models in a Coastal Plain Watershed, Choptank River, Maryland, U.S.A. Proceedings of the ASABE, Paper #:072032, St. Joseph, Mich.:ASABE.

Shedlock, R.J., Denver, J.M., Hayes, M.A., Hamilton, P.A., Koterba, M.T., Bachman, L.J., Phillips, P.J., and W.S. Banks. 1999. Water-quality assessment of the Delmarva Peninsula, Delaware, Maryland, and Virginia- Results of investigations, 1987-1991. Water-Supply Paper 2355-A. Reston, VA: U.S. Geological Survey.

Sutton, A.J. 2006. Evaluation of agricultural nutrient reductions in restored riparian buffers. PhD dissertation. University of Maryland.

Collaborators and Cooperating Agencies and Groups

Carnegie Institution of Washington, Geophysical Laboratory, Washington, D.C.
Chesapeake Research Consortium, Edgewater, Maryland.
Farmers, Maryland's Eastern Shore
Maryland Department of Agriculture, Annapolis, Maryland.
National Oceanographic and Atmospheric Administration, Center for Coastal Monitoring & Assessment, Silver Spring, Maryland.
University of Maryland Cooperative Extension. Wye Research & Education Center, Queenstown, Maryland.
Maryland Department of Natural Resources, Annapolis, Maryland.
Smithsonian Environmental Research Center, Edgewater, Maryland.
University of Maryland Center for Environmental Science, Horn Point Laboratory, Cambridge, Maryland.
University of Maryland, Department of Geography, College Park, Maryland.
U.S. Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, Maryland.
U.S. Department of Agriculture, Natural Resource Conservation Service, Maryland State Office, Annapolis, Maryland.
U.S. Department of Agriculture, Office of Risk Assessment and Cost-Benefit Analysis, Washington, D.C.


Last Modified: 6/16/2009