Bacteria modeling
Shubo Fang
John Beasley
.rch file) in an ArcSWAT simulation, verify that you have properly edited septic systems (incl. WWTP), point source pollution values, manure files, and defined bacteria-related parameters etc., this could result from a few overlooked issues or misconfigurations possibilities?Here's a checklist that I have recommend using to troubleshoot with and hopefully you can receive some positive and viable non-zero bacteria values:
1. Check that the Bacteria Simulation is adequately enabled?
In SWAT, you must explicitly enable bacteria simulation.
In ArcSWAT interface (during project setup), ensure "Bacteria" is selected as a simulated pollutant.
If bacteria is not selected in the simulation options, SWAT will skip all bacteria-related computations regardless of input.
2. Ensure there are Active Bacteria Sources?
Even if you edited source files, SWAT may still interpret those sources as inactive if:
Bacteria concentration in manure is set to zero or near-zero.
Septic or point source loads are zero or improperly formatted.
Land use or management operations don't actually apply the bacteria-containing manure.
Make sure to double-check:
fert.dator management file (*.mgt) for actual manure application dates and amounts.septic.dator point source files for non-zero bacteria loads.
3. Properly confirm and substantiate Proper Routing and Connectivity?
Bacteria must be routed through the landscape to the reach:
Ensure the HRUs and subbasins with bacteria sources are connected to the correct reaches.
Check that runoff and flow are occurring in the same subbasins (no bacteria transport without water).
If there's no flow or no contributing flow to the reach, bacteria will not be transported, hence zero output.
4. Check Simulation Dates and Time Step validity?
Ensure application dates for manure/septic/point sources are within the simulation period.
Verify bacteria sources are applied before or during flow events.
Run for a sufficiently long period to see buildup and transport.
5. Verify all applicable Die-Off and Growth Factors?
If the die-off rate is too high, bacteria may die before reaching reaches.
Check:
bacpar.datfile for die-off and growth parameters.Temperature sensitivity of bacteria decay (if temperature too low, die-off may be rapid).
The die-off factor per day in water and soil should not be unrealistically high.
6. Inspect .rch Output File Settings?
Ensure bacteria is included in the output file. This is configured in
output.subandoutput.rchsettings.Use the SWAT Output Control file (
print.prt) to confirm bacteria is selected.
7. Confirm All Units and Formatting in Input Files?
ArcSWAT uses specific units for bacteria (e.g., CFU per 100 mL).
If values are formatted incorrectly or placed in wrong columns, they’ll be ignored or misread as zero.
8. Locate and Check All Intermediate Outputs?
To pinpoint where bacteria are being lost:
Check HRU outputs (
.hru) to see if bacteria loads are present before routing.Look at subbasin outputs (
.sub) for any bacteria delivery.If values are non-zero in HRUs but zero in
.rch, then loss is during transport (likely due to die-off or filtration).
Summary Fix Steps
| Issue | Fix |
|---|---|
| Bacteria not enabled | Enable in model setup |
| No actual source | Confirm manure application, septic/point source loading |
| Too high die-off | Adjust bacpar.dat values |
| No runoff | Check water balance and land use |
| Bad input formatting | Double-check all bacteria-related files for units and structure |
| Bacteria not routed | Confirm subbasin to reach connection and flow |
On Jul 3, 2025, at 3:53 PM, Shubo Fang <shubof...@gmail.com> wrote:
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Shubo Fang
| From | John Beasley<jpbea...@gmail.com> |
| Date | 7/3/2025 21:24 |
| To | <swat...@googlegroups.com> |
| Subject | Re: Bacteria modeling |