Table of Contents

• Introduction

• Project Overview

• GIS Data Preparation

• Non-Point Bacterial Loading Calculations

• Point Source Bacterial Loading Calculations

• Schematic Processor

• Water Quality Model in Model Builder

• Downloads

• Future Work

• Appendix A: Terrain Preprocessing

• Appendix B: WRAP Hydro Process

• Appendix C: Precipitation Rasters for Land Use Classifications

• Appendix D: Schematic Network

• Appendix E: Process Schematic

• Appendix F: Travel Time Calculations

• Works Cited

• Contact Information

Introduction

Section 303(d) of the 1972 Federal Clean Water Act (CWA) requires that each State identify water bodies that do not meet the State’s water quality standards and create a priority ranking of the impaired waters based on the severity of pollution and the water body’s intended use.

For the State of Texas, the Texas Commission of Environmental Quality (TCEQ) has identified water bodies that do not meet the Texas Surface Water Quality Standards.  Three water bodies that are identified on Texas’ 303(d) list of impaired waters are Copano/Port/Mission Bay, Mission River, and Aransas River, which are all located in the Copano Bay watershed near Texas’ southeastern coastline (shown in Figure 1).  All three water segments do not meet water quality standards due to high bacteria levels. 

Project Overview

In order to meet the State’s water quality (bacterial) standards, the major bacterial sources in the Copano Bay watershed need to be identified; the total bacterial loadings, Total Maximum Daily Loads (TMDLs), from these sources need to be calculated, and the amount of load reductions that is needed to attain water quality standards needs to be estimated.

Arc Hydro tools have been integrated with hydrologic processing engines to create a water quality model to calculate the total point and non-point source bacterial loadings to the Copano Bay watershed.  Using Model Builder in Arc Toolbox, an Arc GIS 9.0 model has been created to determine and accumulate the watershed bacterial loads for each of the impaired water body segments.  Processing engines have also been developed (using dynamic linked libraries or DLLs) to simulate bacterial load transport.

Geographic Information Systems (GIS) Data Preparation

Before calculating the bacterial loadings, watersheds need to be delineated because the bacterial loading per watershed is needed for the Arc GIS 9.0 model.  Watershed delineation requires a Digital Elevation Model (DEM), river network, and Critical Points, which is a feature class that contains points where the fecal coliform concentration can be examined.  Critical Points were determined to be USGS gauge stations, bacteria monitoring stations (so modeled values can be compared to existing monitoring data), and water segment endpoints. 

The DEM was obtained from the National Elevation Dataset (NED) from USGS, which provides seamless coverage of the United States, providing a 1:24,000-scale Digital Elevation Model (shown in Figure 2).  The river network was obtained from the National Hydrography Dataset (NHD), which provides digital spatial data and is based on the USGS Digital Line Graph (DLG) hydrograph data and on information from the Environmental Protection Agency (EPA) Reach File Version 3 (RF3), which is also shown in Figure 2.    The USGS gauge station locations were obtained from BASINS (Better Assessment Science Integrating Point and Non-point Sources), which is an environmental analysis system developed by the U.S. EPA that can be used to perform watershed and water quality studies (shown in Figure 2).  Annual statistics of the flow measured at the gauges found in this watershed were obtained from USGS.  The data and locations of the bacteria monitoring stations and water segment endpoints (shown in Figure 2) were provided by Sandra Alvarado, Natural Resource Specialist for TCEQ, who compiled bacteria data for the three water segments from the TCEQ Texas Regulatory and Compliance System (TRACS) database from the past five years, which includes Texas Department of Health (TDH) data. 

Terrain Preprocessing (found in the Arc Hydro toolbar) needs to be implemented on the DEM (Digital Elevation Model) to determine the flow patterns in the basin (flow direction), and subwatersheds need to be delineated for the Copano Bay watershed based on the Critical Points (USGS gauge stations, water segment endpoints, and bacteria monitoring stations).  After Terrain Preprocessing is complete (procedure found in Appendix A), Water Rights Analysis Package (WRAP) Hydro is used to delineate watersheds for the basin (procedure described in Appendix B).  See Figure 3 for the delineated watersheds.

Non-Point Source Bacterial Loading Calculations

Non-point source bacterial loading calculations were made based on the basic relationship:

L = Q * C

Where:    L = Bacterial Loading (cfu/year), cfu is the number of microbiological organisms (coliform forming units)

               Q = Runoff (m³/year)

               C = Concentration (cfu/m³)

Thus, GIS data layers need to be compiled and prepared in order to calculate Runoff (Q) and Concentration (C). 

Runoff Calculations

Runoff calculations were made by using the empirical equations derived from Ann Quenzer’s thesis, A GIS Assessment of the Total Loads and Water Quality in the Corpus Christi Bay System [1].  These runoff equations were derived by using the Microsoft Excel 5.0 Regressions Tool, which was used to base the equations on a relationship between streamflow depth, precipitation depth and percent land use in each of the nine watersheds in the Corpus Christi Bay system, which includes the Copano Bay watershed.  The annual precipitation data was obtained from the National Resources Conservation Service (NRCS) and the Spatial Climate Analysis Service (SCAS) at Oregon State University (OSU), which is shown in Figure 4.  OSU developed PRISM (Parameter-elevation Regressions on Independent Slopes Model), which gives the average annual precipitation in inches from 1961-1990.  The land use land cover dataset was obtained from the United States Geologic Survey (USGS) and was developed from national land cover data from Multi-Resolution Land Characterization (MRLC) data called National Land Cover Data 1992 (NLCD 92) and is based on 30-meter Thematic Mapper data.  These are the following equations that were used to predict runoff based on land use classifications.

Agriculture:

Q = 0.008312 * exp ( 0.011415 * P )

Forest:

Q = 0.0053 * exp ( 0.010993 * P )

Urban:

Q = 0.24 * P

Open Water:

Q = 0

 Where:    Q = Runoff (mm/year)

                P = Precipitation (mm/year) – from PRISM

The precipitation data was obtained from PRISM in polygon feature class format.  Using the “Feature to Raster” tool in Arc Toolbox, the polygon feature class was converted to a raster based on the field, “RANGE”, which is the annual precipitation in inches.  The annual precipitation was then converted to millimeters by using Spatial Analyst's Raster Calculator: [Precipitation in in/year] * (25.4 mm/inch) = [Precipitation in mm/year] = P, where [] represents a raster.

Precipitation rasters were then created for each land use classification (Agriculture, Forest, Urban, and Open water).  The procedure for how this was done is described in Appendix C.  Once the Precipitation rasters, P, for each land use are created, Raster Calculator can be used to calculate the runoff for each land use.  Figure 5 shows an example of how the Runoff raster for Agriculture is calculated based on Ann Quenzer’s runoff equations: 

Once the four Runoff rasters are created for each land use, the “Mosaic” tool in Arc Toolbox was used to combine all four rasters into a single Runoff raster.

Once the total Runoff raster is created (Q_total in mm/year), the Raster Calculator needs to be used to convert the runoff into m³/year.  Because the raster contains 30m by 30m grid cells, a conversion factor of 0.9 needs to be used. [Runoff in mm/year] * 0.9 = [Runoff in m³/year].

Event Mean Concentratin (EMC) Calculations

GIS data layers that were used to calculate the bacteria concentration in the Copano Bay watershed.  The land use land cover dataset was obtained from USGS, and the EMC values (fecal coliform concentrations) can be approximated for each type of land use.  For this project, fecal coliform EMCs for each land use code were determined by Reem Jihan Zoun in her thesis, Estimation of Fecal Coliform Loadings to Galveston Bay (2003) [2], which are listed in Table 1 below.  However, fecal coliform EMC values for land use classifications 51 (Shrubland), 71 (Grasslands/Herbaceous), and 81 (Pasture/Hay) were modified to zero in order to not account twice for the bacterial waste produced from livestock animals.  Fecal coliform bacterial loadings from livestock are accounted for in Point Source Bacterial Loading Calculations.

                                                           Table 1. Fecal Coliform EMC values based on Land Use Classifications [1]

 The Source Code descriptions for EMC values in Table 1, also found in Zoun’s thesis [2], are given in Table 2.

                                                           Table 2. Description of Source Code for EMC values

The Event Mean Concentration (fecal coliform concentration) raster is created by using the relationship between fecal coliform concentrations and land use found in Table 1.  Once the EMC table (Table 1) is joined to the land use land cover feature class based on the land use codes (found in both EMC Table and the Land Use Land Cover Polygon Feature Class), a raster can be created based on the EMC field (now in the land use land cover feature class) using the “Feature to Raster” tool in Arc Toolbox.  Raster Calculator then needs to be used to convert cfu/100mL to cfu/m³. [cfu/100mL] * 10,000 = [cfu/m³].

Non-Point Source Bacterial Loading Calculations

The bacteria load per grid cell can now be calculated by using Q and C rasters created from Runoff Calculations and EMC Calculations: L = Q * C, using Raster Calculator.

Using Zonal Statistics and the delineated watersheds (Figure 3), the cumulative runoff and bacterial loadings can be calculated for each watershed.  Figure 6 shows the results. 

Point Source Bacterial Loading Calculations

The point sources that may contribute to fecal coliform bacteria contamination to the Copano Bay watershed are livestock, wastewater treatment plants (WWTPs), colonial waterbirds, leaking septic systems, confined animal feedlot operations (CAFOs), and so forth.

Concentrated Animal Feedlot Operations (CAFOs)

A shapefile that contains the two permitted CAFOs within the Copano Bay watershed was obtained from the TCEQ.  However, one of the permitted facilities is actually located within the Nueces River Basin and drains to Lake Corpus Christi and not Copano Bay.  The other permitted facility is in the Copano Bay watershed, but the permit was not recently renewed because the company is no longer operating (Personal Communication with CAFO Permitting Team Leader, Beth Fraser.)  Thus, there are no CAFOs within the Copano Bay watershed at this time.

Livestock

Livestock data (annual count per county) were obtained from the 2002 Census of Agriculture, National Agricultural Statistics Service (NASS), and the 2004 Texas Livestock Inventory and Production, United States Department of Agriculture (USDA), NASS, Texas Statistical Office.  The animals that were considered in the calculations were cattle, goats, horses, sheep, hen, hogs, and chickens.  For example, in 2002, there were 22,253 cattle in San Patricio County.

The density of livestock per county (count/m²) were calculated for each animal by using the following equation: [Total annual count of each animal] / [Area in m² where the animals would be located within county].  The area where animals would be located was assumed to be from the land use land cover values 51 (Shrubland), 71 (Grasslands/Herbaceous), and 81 (Pasture/Hay).  To find the area, the land use land cover dataset needs to be masked by each county, and the corresponding grid cells need to be summed.  For example, in San Patricio County (calculation shown in Figure 7), the total area where animals are located is 177,403,500 m².  Thus, the density of cattle in San Patricio county is 22,253 cattle/177,403,500 m² = 0.000125 cattle/m².

The area (m²) of each county within each delineated watershed (Figure 3) was determined and then multiplied by each livestock's density in each corresponding county.  For example, Watershed JunctionID 45422 has two counties overlapping it, so there are two different areas and cattle densities to account for.  The calculation of how many cows are in Watershed JunctionID 45422 is shown in Figure 8.  Thus, there are approximately 14,366 cattle in Watershed JunctionID 45422.

After determining the count of each animal within each watershed, the count is multiplied by the cfu/year produced by each animal.  Table 3 shows the cfu/year produced by each animal that is considered in this bacterial loading model.

Table 3. Annual Fecal Coliform Bacterial Loading (cfu/year) for Livestock Animals

For example, in Watershed JunctionID 45422: 14,366 cows * (1.97 x 10¹² cfu/year cow) = 2.78 x 10¹⁶ cfu/year from cattle.  The cfu/year needs to be summed for all species within each watershed.  The total cfu/year for each watershed then needs to be added to the non-point bacteria loading calculations to obtain the total cfu/year in each watershed as shown in Figure 9.

Wastewater Treatment Plants (WWTPs)

The locations of WWTPs were obtained from the Permitted Wastewater Outfalls shapefile provided by the TCEQ.  Descriptions of the permitted facilities were obtained from Sandra Alvarado from the TCEQ TRACS database.  The average cfu/year from the WWTP monitoring data were determined and compared to cfu/year values from literature.  However, WWTPs must be in compliance with surface water quality standards and disinfect the bacteria in the wastewater effluent.  It is assumed that the fecal coliform bacteria in the effluent is disinfected before being discharged into the surface waters.

Septic Systems

The number of septic systems per county was obtained from the U.S. Census of Bureau 2000 for the Copano Bay watershed, but the exact locations were not determined.  However, this data does not include possible leakages in the septic systems.  

The Comprehensive Sanitary Survey of the Shellfish Producing Waters of Copano Bay [3] gives approximate locations of septic systems around the Copano Bay area and reports minimal leakage from the septic systems surrounding the Bay.

The work of Dr. Joanna Mott, Texas A&M - Corpus Christi, which shall be complete by the end of July, will identify the possible sources that the bacteria is coming from (using Bacteria DNA fingerprinting; also known as bacteria source tracking).  Pending on the results of Dr. Mott's study, the density of septic systems may be significant (if the bacteria contamination is primarily from human feces.)  This would indicate that there may be possible leakage in septic systems where fecal coliform bacteria contamination is the greatest.

Thus, septic system leakages are not going to be accounted for in the bacteria loading model (due to lack of leakage data), but the septic system concentration within each county may be critical if there are no other sources in the area that may account for the high fecal coliform concentrations.

Schematic Processor

Once the bacteria loadings are calculated per watershed (accounting for both point and non-point bacterial loadings), the transport of bacteria from the watersheds to Copano Bay needs to be modeled.  In order to simulate bacterial load transport, “Process Schematic” (a script tool that was developed by Jon Goodall and Tim Whiteaker in 2003) implements dynamic linked libraries (DLLs).  The two processing engines (DLLs) that were used in this bacteria watershed model were clsDecay.dll, which accounts for first-order decay of bacteria along water segments, and clsCFSTR.dll, which calculates the increase in bacteria concentration in Copano Bay due to bacteria loadings from the upstream watersheds.  Goodall and Whiteaker submitted a journal article describing the Schematic Processor and Schematic Network in more detail for publication in Transactions in GIS called  "Integrating Arc Hydro Features with a Schematic Network".  The journal article can be viewed here.

Schematic Network

Before the “Process Schematic” tool can be implemented, a Schematic Network of the Copano Bay watershed needs to be created, and the procedure is described in detail in Appendix D.  The Schematic Network is made up of two feature classes: SchemaNode and SchemaLink.  SchemaNode represents the nodes in the watershed (a watershed, drainage point, or Copano Bay.)  SchemaLinks connect the Schematic Nodes and is a way to model what happens to the bacteria as it travels to Copano Bay.  Figure 10 shows the Schematic Network that was created for the Copano Bay watershed and includes the necessary parameters (inputs) necessary to run the model that are explained in more detail in Appendix D and below in Dynamic Linked Libraries (DLLs).

Dynamic Linked Libraries (DLLs)

clsDecay.dll simulates decay of bacteria along stream segments (shown in Figure 11) and assumes first-order decay by the following equation:

 load_passed = load_received * e^-kt

 Where:    k = first-order decay coefficient (day^-1), which is stored as an attribute in SchemaLink

                t = travel time (residence time) along streams, t (days), which is stored as an attribute in SchemaLink

clsCFSTR.dll calculates the increase in concentration of a bay due to bacteria loadings.    The bay is assumed to be completely mixed and acts as Continuous Flow, Stirred Tank Reactor (CFSTR), and the inflow into the bay equals the outflow.  The following equation calculates the concentration in the bay:

 c = L / (Q + kV) 

Where: c = concentration in bay (cfu/m³)

            L = bacteria load entering bay (cfu/year)

            Q = total flow (m³/year), which is stored as an attribute in SchemaNode

            k = first-order decay coefficient (day^-1), which is stored as an attribute in SchemaNode

            V = Volume of bay (m³), which is stored as an attribute in SchemaNode                                            

Once the Schematic Network is created and the parameter values are input to the corresponding fields in the attribute tables of SchemaNode and SchemaLink, “Process Schematic” can be run (see Appendix E).

Water Quality Model in Model Builder

All the processes previously described were also modeled in Model Builder (non-point bacterial loading calculations) as seen below in Figure 12.

A summary of Model Builder (where the tools, inputs, and outputs can be viewed) and diagrams of what each step in Model Builder does is shown here.  After running the final step, the Schematic Processor, the bacterial loadings and concentrations can be determined for each SchemaNode and SchemaLink.

Downloads

The model (Figure 12), along with all the necessary data, DLLs, and scripts needed to run the model, can be downloaded in the following zip file:

• BacterialModel.zip

  • Water Quality Model (using Model Builder)

    • Includes model in Model Builder, necessary tools, DLLs, and "Process Schematic" script.

  • Personal Geodatabase

    • Contains all the necessary data to run Model Builder for Copano Bay Non-point Bacterial Loading Model

Future Work

These are the following tasks that need to be completed:

• The colonial waterbird fecal loads (point sources) need to be incorporated into the non-point bacterial loading model.

• The residence time, t, for each river segment needs to be determined. 

• The decay coefficients, k_d, need to be determined for each river and bay segment (taking into account critical factors, such as sunlight intensity/duration, water temperature, dissolved oxygen (DO), and salinity effects.) 

• The model needs to be calibrated by adjusting the critical parameters k_d and t to obtain plots (fecal coliform concentration versus standard normal variable, Z) to agree with the bacteria monitoring data at each bacteria monitoring station.  Once the model is calibrated, it needs to be confirmed that the k_d and t values are reasonable. 

• Once the model is calibrated and the parameter values are reasonable, the current load, allowable load, and the load reductions necessary to meet water quality standards for each TCEQ water segment (e.g., 2001, 2003, 2472) need to be determined.

• Dr. Joanna Mott's findings, which will hopefully identify the primary species that the bacteria is coming from, are expected sometime in July and will be reviewed and incorporated into the final report.

Appendix A

 Terrain Preprocessing

For this project (and in order to use WRAP Hydro), the only steps that need to be implemented from Terrain Preprocessing (located in the Arc Hydro Toolbar) are DEM Reconditioning, Fill Sinks, and Flow Direction.  Before starting the process, the DEM was clipped to the watershed basin by going to Spatial Analyst | Options and changing the “Analysis Mask” to the subbasin feature class.  Then go to Spatial Analyst | Raster Calculator and evaluate the DEM to obtain the clipped DEM.

 DEM Reconditioning

1. Select Terrain Preprocessing | DEM Reconditioning.

2.  Select the clipped DEM as the “Raw DEM”.

3. Select the modified NHDFlowline (with all the river segments connected) as the “Agree Stream”.

4. Keep all the default settings, and the output will be “AgreeDEM”.

5.  Press OK, and the “AgreeDEM” layer will be added to the map.

Fill Sinks

1. Select Terrain Preprocessing | Fill Sinks.

2. Select AgreeDEM as "DEM".

3. Keep all the default settings, and the output will be "Fil".

4. Press OK, and the "Fil" layer will be added to the map.

Flow Direction

1. Select Terrain Preprocessing | Flow Direction.

2. Select Fil as “Hydro DEM”.
3. Keep all the default settings, and the output will be “Fdr”.
4. Press OK, and the “Fdr” layer will be added to the map.

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 Appendix B 

WRAP Hydro Process

Water Rights Analysis Package (WRAP) Hydro, which is a toolbar located in Arc GIS, is used to delineate watersheds for the basin.  The watersheds were delineated to the Critical Points (USGS gauge stations, water segment endpoints, and bacteria monitoring stations.)

Create Geometric Network

1. Using Arc Catalog, create a personal geodatabase called “WRAPHydro” within a chosen directory.
2. Create a feature dataset (called “WRAPHydro”) within the Geodatabase, and use the projection: NAD 1983 Texas Centric Mapping System Albers (this will maintain the area, which is crucial in maintaining drainage areas for non-point source calculations.)
3. Import NHDFlowline (with all the river segments connected) into the feature dataset, and rename it “WRAPFlowline”.
4. Import “CriticalPoints”, which is the created feature class that contains the USGS gauge stations, bacteria monitoring stations, and water segment endpoints. (Note: before creating a geometric network, the Editor Toolbar in Arc GIS needs to be implemented to ensure that all the critical points are connected to the river network (WRAPFlowline). “Critical Points” is the target layer, and “Modify Feature” is the task.  Go to Editor | Snapping… and check the box to allow the critical points to snap to the edge, WRAPFlowline.  This allows one to move and snap the critical points to WRAPFlowline.
5. Right-click on the feature dataset in Arc Catalog, and go to New | Geometric Network…
6. Hit “Next”, and select “Build a geometric network from existing features.”
7. Select “WRAPFlowline” and “CriticalPoints”, name the geometric network, and hit “Next”.
8. Select “Yes”, so the complex edges will be in the network.
9. Keep all the default settings for the rest of the options, and hit “Finish”.

Assign HydroIDs to the Edges

1. In the Arc Hydro Toolbar in Arc Map, go to Attribute Tools | Assign HydroID.
2. Select the WRAPFlowline and CriticalPoints layers.
3. Say “Yes” to overwrite existing HydroIDs, apply to selected features, and press “OK”.

Delineate Watersheds

1. Make sure the WRAP Hydro Toolbar is open in Arc Map.
2. Set spatial extent.
3. Using the Spatial Analyst Toolbar, go to Spatial Analyst | Options…
4. Select the “Extent” tab, and make sure that the Fdr or DEM grid is selected for the Analysis Extent.
5. Set flow direction.
6. Using the Arc Hydro Toolbar, go to Network Tools | Set Flow Direction…
7. Select the WRAPFlowline layer and assign based on Fdr (flow direction grid that was created in Terrain Preprocessing) attribute, and press “OK”.
8. Using the WRAPHydro Toolbar, go to Settings | Layers
9. Set “WRAPJunction” to CriticalPoints.
10. Set “HydroEdge” to WRAPFlowline.
11. Set “Flow Direction Raster” to Fdr.
12. Go to Options | Delineate Watershed.
13. Set “Source Layer” as WRAPFlowline.
14. Set “Source Attribute” as JunctionID.
15. Set the Drainage Area Units as square meters.
16. Click on “Batch Process WRAPJunctions” from the WRAP Hydro menu to delineate the watersheds.
17. Clip the watersheds, so that Copano Bay is excluded from the watershed areas.

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 Appendix C

 Precipitation Rasters for Land Use Classifications

 In order to calculate the runoff for each land use classification, the precipitation grid needs to be divided into four different rasters based on land use classifications.

Create Feature Classes of Different Land Uses

1. Use “Raster to Polygon” tool in Arc Toolbox to convert the land use land cover raster to a polygon feature class.
2. Right-click on land use land cover feature class (in Arc Map), go to Properties | Definition Query.
3. Select “Query Builder…”
4. Double-click on [GRIDCODE] (the field that contains the land use codes), “=” and select one of the grid code values that can be classified as either Agriculture, Forest, Urban, or Open Water.  If there are multiple grid codes that could be Agriculture, Forest, Urban, or Open Water, click “AND”, and repeat step 4. (Note: what grid codes are associated with which land use classification is open to interpretation.)
5. After conducting a query for one of the land use classifications, then select all the polygons in the Arc Map view.
6. Right-click on the land use land cover polygon feature class, and Data | Export Data… and create a new feature class for that specific land use classification.
7. Repeat steps #4-6 until you have four new feature classes (Agriculture, Forest, Urban, and Open Water.)

Create Precipitation Rasters for Land Use Classifications

1. Go to Spatial Analyst | Options…
2. Set the “Analysis mask” to one of the land use classification feature classes (Agriculture, Forest, Urban, Open Water).
3. Set the “Extent” and “Cell Size” to the land use land cover raster.
4. Go to Spatial Analyst | Raster Calculator…
5. Double-click on the precipitation raster, P, and “Evaluate”.
6. Right-click on the Calculation raster and Make Permanent.
7. Repeat steps #1-6 for the other three land use classifications. (You will now have the original precipitation raster divided into four precipitation rasters based on the four different land use classifications.)

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 Appendix D 

Schematic Network

In order to run the “Process Schematic”, a Schematic Network of the Copano Bay watershed needs to be created.  The Schematic Network consists of two feature classes: SchemaNode and SchemaLink.

 Creation of Automated Schematic Network 

1. Go to Arc Hydro Toolbar, go to Network Tools | Node/Link Schema Generation.
2. Set the Watershed Polygons as the delineated watersheds that were created (Figure 3), and the Junctions as BatchPoint (the feature class that contains the critical points: USGS gauge stations, bacteria monitoring stations, and water segment endpoints). (Note: the feature classes SchemaLink and SchemaNode will be automatically created.)

Modify Automated Schematic Network

Because of the complex network (due to Copano Bay), the SchemaLink and SchemaNode attributes will need to be manually modified.

SchemaNode Modifications

1. Go to Editor | Start Editing…, and edit within the Personal Geodatabase that contains the SchemaLink and SchemaNode feature classes.
2. Set the Task as “Create New Feature” and the Target layer as “SchemaNode”.
3. Add junctions in the middle of each of the watersheds, drainage points (BatchPoint), and four junctions in Copano Bay; (Copano Bay was divided into four segments.)
4. Open the attribute table of the SchemaNode feature class, and set the SrcType for each of the junctions (1 = Watershed, 2 = Junction watershed drains to, 3 = Copano Bay.)
5. Open the attribute table of the SchemaNode feature class, and set the FeatureID for each of the watershed junctions (SrcType = 1) to the JunctionID of the corresponding watershed.
6. Go to Editor | Stop Editing, and save edits.

SchemaLink Modifications

1. Go to Editor | Start Editing…, and edit within the Personal Geodatabase that contains the SchemaNode and SchemaLink feature classes.
2. Set the Task as “Create New Feature” and the Target layer as “SchemaLink”.
3. Add links, so that all the SchemaNode feature classes are connected by a SchemaLink. (Go to Editor | Snapping…, and select the Vertex, Edge, and End boxes of the SchemaNode feature class, so the endpoints of SchemaLink will snap to the SchemaNodes.)
4. Open the attribute table of the SchemaLink feature class, and set the LinkType for each of the links (1 = Connects watershed to drainage junction, 2 = Connects drainage junction to drainage junction, 3 = Connects drainage junction to Copano Bay.)
5. Go to Editor | Stop Editing, and save edits.
6. Go to the Arc Hydro toolbar, and go to Attribute Tools | Assign HydroID, and assign HydroIDs for the SchemaNode and SchemaLink feature classes.
7. Start the Editor, and edit the SchemaLink feature class.
8. Open the SchemaLink attribute table, and populate the fields FromNodeID and ToNodeID with the corresponding HydroIDs of the upstream and downstream SchemaNodes.
9. Go to Editor | Stop Editing, and save edits.

 Schematic Network Parameters

Before the Schematic Network is complete, fields need to be added to the attribute tables of the SchemaNode and SchemaLink feature classes.

SchemaLink

1. Open the attribute table of the SchemaLink feature class, and go to Options | Add Field…
2. Repeat part (a) until all the following fields are added:

                                                               i.      Name: “DecayConst_day”, Type: “Double”

                                                             ii.      Name: “TravelTime_day”, Type: “Double”

                                                            iii.      Name: “TotVal”, Type: “Double”

                                                           iv.      Name: “PassedVal”, Type: “Double”

                                                             v.      Name: “IncVal”, Type: “Double”

3. Using the Editor Toolbar, the following fields need to be populated for LinkTypes 1 and 2: “DecayConst_day” and “TravelTime_day”.

                                                               i.      For preliminary work, the “DecayConst_day” was assumed to be 1.5 day^-1, which is the decay constant associated with fecal coliform bacteria in fresh river water at 20ºC (Bogosian et al., 1996).

                                                             ii.      For preliminary work, the “TravelTime_day” was determined by using the relationship Time = Flow Length / Velocity, and the procedure of how this was determined can be found in Appendix F.

SchemaNode

1. Open the attribute table of the SchemaNode feature class, and go to Options | Add Field…
2. Repeat part (a) until all the following fields are added:

                                                               i.      Name: “DecayCoef_day”, Type: “Double”

                                                             ii.      Name: “FLOW_m3_yr”, Type: “Double”

                                                            iii.      Name: “Volume”, Type: “Double”

                                                           iv.      Name: “TotVal”, Type: “Double”

                                                             v.      Name: “PassedVal”, Type: “Double”

                                                           vi.      Name: “IncVal”, Type: “Double”

3. Using the Editor Toolbar, the following fields need to be populated for SrcType 1:

                                                               i.      “IncVal” - The values that should populate this field are the total bacterial loadings (cfu/year) per watershed. (“IncVal” = cfu/year of corresponding watershed (FeatureID of SchemaNode = JunctionID of watershed)).

4. Using the Editor Toolbar, the following fields need to be populated for SrcType 3:

                                                               i.      “DecayCoef_day” - for this term project, the “DecayCoef_day” was assumed to be 1.5 day^-1, which is the decay constant associated with fecal coliform bacteria in fresh river water at 20ºC (Bogosian et al., 1996).  

                                                             ii.      “Volume” – the volume of the four segments was determined by first dissolving the water quality segments determined by George Ward and Neal Armstrong in Corpus Christi Bay National Estuary Program's (CCBNEP) Ambient Water, Sediment and Tissue Quality of Corpus Christi Bay Study Area: Present Status and Historical Trends [4] into four segments. The depth of these segments was determined using bathymetric maps.  Thus, the volumes were determined by multiplying the surface area of each of the segments by the average depth.

                                                            iii.      “FLOW_m3_year” – this is the cumulative runoff of the upstream watersheds to each Copano Bay segment and was found by summing the runoff from all the upstream watersheds draining to each of the four Copano Bay segments.

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 Appendix E

Process Schematic

Once the Schematic Network is created, the input feature classes, corresponding fields, and DLLs need to be set in the Process Schematic as can be seen below.  This set-up is telling the script (Process Schematic) to implement decay (clsdecay.dll) on SchemaLink LinkTypes 1 and 2 (will decay bacteria as they travel from the watersheds to the streams and decay bacteria as they travel along the streams), and run a CFSTR model (clsCFSTR.dll) on SchemaNode SrcType 3 (Copano Bay waters segments).

Note: Each row (as seen below) corresponds to the same row of the following fields.  For example, the Processing Op in the first row, WaterQualityProcessors.ClsDecay (clsdecay.dll), simulates decay of the bacteria loadings along LinkType 1 (Op Source Type) and passes the value (Op Behavior Type: Pass).

Run Process Schematic

1. Right-click on “Process Schematic”, and Run.
2. Results are found in the attribute tables of SchemaLink and SchemaNode (under the fields: PassedVal and TotVal). 
   1. SchemaNode
      1. Src Type 2
         1. The populated values in the "PassedVal" and "TotVal" fields are bacterial loadings (cfu/year).
         2. These values can be converted to cfu/m³ by dividing by the cumulative upstream runoff (m³/year), and this concentration can be converted to cfu/100mL by dividing by 10,000.
      2. Src Type 3
         1. The populated values in the "TotVal" field are bacterial concentrations in cfu/m³.
         2. This value can be converted into bacterial loading (cfu/year) by multiplying by the cumulative upstream runoff (m³/year) to that SchemaNode.

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Appendix F

 Travel Time Calculations

The travel times for Link types 1 and 2 need to be determined to run the Schematic Processor.  The following equation was used to calculate travel time:

 Travel Time = Flow Length / Velocity

 Flow Length calculations

1. Create Fdr (Flow Direction Raster that was created during Terrain Preprocessing, Appendix A, with the Digital Elevation Model, DEM) that does not include Copano Bay.
2. Create polygon feature class of subbasin with Copano Bay omitted.

                                                               i.      Use “Union” tool under Analysis tools to combine the feature classes: Copano Bay and the subbasin.

                                                             ii.      Using the Editor Toolbar, delete Copano Bay from the created feature class, and save edits.

3. Go to Spatial Analyst | Options…, and set the “Analysis Mask” to the feature class that was created in step a.
4. Set the “Extent” and “Cell Size” to the Fdr raster.
5. Go to Spatial Analyst | Raster Calculator…
6. Double-click on the Fdr raster, and “Evaluate”.
7. Right-click on the Calculation raster and Make Permanent.
8. Create flow length raster.
9. In Arc Toolbox, go to the Spatial Analyst Tools, and open the tool “Flow Length”.
10. Select the Fdr raster (with Copano Bay omitted) as the “Input flow direction raster”.
11. Choose the name and directory for which the raster is to be placed.
12. Set the “Direction of measurement” to DOWNSTREAM, and press “OK”.
13. The flow length from each grid cell to Copano Bay is then calculated.
14. Determine mean flow length in each delineated watershed.
15. Go to “Zonal Statistics as Table”.
16. Select the delineated watersheds (Figure 3) as the “Input raster or feature zone data”.
17. Set the “Zone field” to JunctionID (the identifier for each watershed).
18. Set the “Input value raster” to the flow length raster that was created in step #2.
19. Choose the name and directory for which the table is to be placed.
20. Join table created in step #3 (Flow Length Statistics Table) to the watershed feature class.
21. Go to CRWR Attribute Tools in Arc Toolbox and use the tool: “Copy Field to Feature Class from Table” that was created by Nate Johnson (2004).
22. Join based on JunctionID (field in Watershed feature class) and VALUE_ (field in Flow Length Statistics Table that correlates with JunctionID) and add the field, MEAN, from the Statistics Table, which will give the mean of the flow length values within each delineated watershed.
23. For SchemaLink (Link type 1), the flow length (from the watershed to the stream) was calculated by: {Mean flow length of the watershed} – {flow length at the drainage junction (SchemaNode Srctype 2) determined from FlowLength raster}.
24. Open the attribute table of the delineated watershed feature class.
25. Go to Options… | Add Field

    1. Name: “FlowLength”, Type: “Double”.

26. Go to Editor | Start Editing…, and edit within the Personal Geodatabase that contains the delineated watersheds (Figure 3).
27. Open the attribute table of delineated watershed feature class, and manually input the flow lengths for each of the links (LinkType 1) as explained in the statement in step #5.
28. Go to Editor | Stop Editing, and save edits.
29. For SchemaLink (Link type 2), the flow length along the streams was calculated by: {Flow length at upstream SchemaNode} – {Flow length at downstream SchemaNode}.
30. Go to Editor | Start Editing…, and edit within the Personal Geodatabase that contains the delineated watersheds (Figure 3).
31. Open the attribute table of delineated watershed feature class, and manually input the flow lengths for each of the links (LinkType 2) as explained in the statement in step #6.
32. Go to Editor | Stop Editing, and save edits.

 Velocity Calculations

For preliminary work, velocities of the streams were determined using the flow – velocity relationships similar to the work of Zoun [2].  The relationship between flow and velocity was derived from the EPA Reach File 1 (RF1) database, which documents flow and velocity for the entire United States.  A regression line was fitted to the flow and velocity data for the Copano Bay watershed area (same method Zoun used to derive flow and velocity relationship in Galveston Bay area).  These following equations were used to calculate the velocity for each of the stream segments (SchemaLinks).

V = 63.252 * Q ^0.3132

 Where:             V = velocity in m/day

                        Q = flow in m³/year

 The cumulative runoff at each upstream and downstream SchemaNode were averaged for each SchemaLink, and then plugged into the above equation.

1. Add Velocity field to SchemaLink feature class.
2. Go to Options… | Add Field. (Name: “Velocity”, Type: “Double”).
3. Go to Editor | Start Editing…, and edit within the Personal Geodatabase that contains the Schematic Network.
4. Open the attribute table of the SchemaLink feature class, and manually input the velocities (calculated from above equation) for each of the links as explained in the statement in step #1.
5. Go to Editor | Stop Editing, and save edits.

 Travel Time Calculations

1. Open the attribute table of the SchemaLink feature class.
2. Right-click on the field: “TravelTime_day”
3. Double-click on the flow length field, push the “ / ” button, and double-click on the velocity field in order to calculate: TravelTime_day = FlowLength/Velocity.

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 Works Cited

[1]       Quenzer, Ann Marie. “A GIS Assessment of the Total Loads and Water Quality in the Corpus Christi Bay

                    System.” University of Texas at Austin, 1997.

[2]       Zoun, Reem Jihan. “Estimation of Fecal Coliform Loadings to Galveston Bay.” The University of Texas at

                    Austin, 2003.

[3]        "Comprehensive Sanitary Survey of the Shellfish Producing Waters of Copano Bay." Texas Department of

                    Health, Seafood Safety Division, 2000.

[4]        Ward, George H., and Neal E. Armstrong. "Ambient Water, Sediment, and Tissue Quality of Corpus

                    Christi Bay Study Area: Present Status and Historical Trends." Center for Research in Water

                    Resources: The University of Texas at Austin, 1997.

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Contact Information

Carrie Gibson, E.I.T.

Graduate Research Assistant
Center for Research in Water Resources
Department of Civil Engineering, The University of Texas at Austin
cjgibson@mail.utexas.edu
 

These materials may be used for study, research, and education, but please credit the authors and the Center for Research in Water Resources, The University of Texas at Austin. All commercial rights reserved. Copyright 2005 Center for Research in Water Resources.