SAN JOAQUIN RIVER Dissolved Oxygen Total Maximum Daily Load Stakeholder Process

Note:  Please send any comments on these notes at your earliest
opportunity.  Thank you.  Kevin
*********

San Joaquin River Dissolved Oxygen TMDL
Technical Committee Meeting - DRAFT 1 Notes
Rough Cut Loading Analysis
December 13, 1999

Attending:  Doug Ball (USBR), Doug Brewer (JSA), Russ Brown (JSA), John
Fleming (Western United Dairymen), Chris Foe (RWQCB), Alex Hildebrand (SDWA
and BDAC), Jay Jahangiri (Port of Stockton) Brant Jorgenson (JSA), Vance
Kennedy (Farm Bureau), Tom King (RWQCB), Charlie Kratzer (USGS), G. Fred
Lee (advisor to DeltaKeeper), Peggy Lehman (DWR), Gary Litton (UOP), Paul
Marshall (CalFed), Frank Motzkus (Tracy), Bob Murdoch (Stockton), Casey
Ralston (DWR), Rich Stowell (Eco:logic, F.B.), Wangteng Tsai (Systech),
Erwin Van Nieuwenhuyse (USFWS, AFRP), Kevin Wolf (facilitator and notes)

Next Meeting: 
1. To be determined.  Expect it in early January.

A. Next Steps
1. All responsible people will send their final drafts reports to Fred for
incorporation into the synthesis report.  These individual reports will be
added as appendices in the final.  

2. Kevin will review all notes from previous meetings to incorporate
questions and issues in their appropriate category.  In addition, he will
send out note from this meeting. 

3.  Other people will provide information as noted through these notes.

B. Mossdale to Channel Point - Tom King
1. Tom King estimates that the average daily load is 15,000 pounds per day
of BOD.  Some of the concerns about this calculation include:
a. How does this load estimate account for the lab test for B.O.D. and the
fact that the test keeps the algae covered and in the dark while algae in
the river gets some light and gains air from the surface?  Does the B.O.D.
test overestimate the load?  What is the ultimate BOD for water sampled in
this area, not just the 30-day BOD?  

b. Algae decompose quickly.  How does the load estimate account for changes
in algal breakdown chemicals based on different flows and residency times?
(For more discussion, see D3a.)

c. A number of drains empty differing amounts of load into the river
between Mossdale and Channel Point.  In addition there are diversions in
this section that decrease the load as flows are diverted to agricultural
fields.  We will likely need to identify all discharge sources to and
diversions from the river from Vernalis to Mossdale and from Mossdale to
Channel Point in order to determine how much of an impact they have
cumulatively.  For example French Camp Slough provides up to 5% of the flow
when the river is running around 1000 cfs, though it could be up to 30% or
more when flow drops to 150 cfs as it did at the end of September.  (Note:
Tom was asked to check his French Camp flow estimates against the measured
flows from the current gage in the slough.)

d. Most critical to the below-Mossdale load estimate is an accurate
calculation of river flows.  The UVM device at Channel Point is estimated
to be accurate to plus or minus 20%.  One way to help verify the river's
flow is to have flow measured on the Old River downstream of the split.
Using this in combination with the upstream flow measurement at Vernalis
and downstream measurements in the main river will help provide a more
accurate estimate of flow and load into the DWC.  The USGS should be asked
for the confidence interval for their flow measurements at Mossdale.

e. How accurate are the B.O.D. measurements at Vernalis?  This could be a
source of error in the load estimate.  Also, how much load is added to the
river between Vernalis and Mossdale and is any removed through diversions
(besides at the Old River)?  The New Jerusalem Drain enters the river
between these locations.  Are there any food processing plants that drain
to the river here?

2. Additional monitoring and research should occur in the Mossdale to
Channel Point section of the river in order to help determine what occurs
through this stretch.  For example:
a. Are there large clam beds that may be consuming the algae in this
stretch of river? 

b. Are diatoms more readily biodegradable in this reach of the river
because it is in a more disturbed state due to the influences of tidal
flows?  How do the diatoms affect the load estimate and the BOD tests?

c. Where does the load go?  Does it all reach the DWC or is some removed
through diversions in this stretch of the river?

d. Flows should be estimated over the course of a full tidal cycle and not
just on a daily basis.  Can automated monitoring help?  This would help in
determining the residence time between Mossdale and the DWC.

C. Monitoring in the Deep Water Channel - Peggy Lehman
1. Up to the present time, the river continues to have low D.O. levels
between the beginning of the DWC to around Disappointment Slough downstream
where the Sacramento River enters the river.  It is thought that the D.O.
improves below Disappointment Slough because of the improved water
conditions that occur downstream of where the large amount (and higher
quality?) Sacramento River water mixes with the San Joaquin flows.  There
are a number of issues and questions related to Sacramento River water's
impact on D.O.  They include:

a. A significant percentage (X%) of the Sacramento River's flow is pulled
upstream to the state and federal export pumps (and Contra Costa's pumps?)
in the south.  Does it make a difference in what channels the Sacramento
River water travels south?

b. How does the opening and closing of the Delta Cross Channel affect
Sacramento R. water flows and D.O. conditions?  How will future operations
of the DCC impact D.O. levels?

c. How doe South Delta Barrier operations affect Sacramento River flows
through this section of the Lower River and DWC?

2. Water temperatures dropped in October and November and are now around 17
degrees in the middle of December, yet D.O. levels are still below 5.
Something is still exerting O2 demand while the capacity of the water for
D.O. is increasing as the temperature drops. 

3. In-flows and loads from the sloughs around Stockton, from the Calaveras
River and from Delta Island discharges are not quantified nor included in
the analysis of how D.O. levels change in the DWC.  They may or may not be
significant contributors to the problem.  In addition, what is the impact
of the "first flush" of urban areas that occurs with the first rains of the
season when this runoff enters the river and the DWC area?

4. More analysis is needed to split out the RWCF load and flows from the
Channel Point monitoring data to get the river-only contribution to the DWC
load and flow.

5. Especially when river flows drop, determining the fate of RWCF's
discharged ammonia will be important.  How much of it ends up as nitrate in
the river and DWC and what is its impact on D.O.?  

6. Suggestions are needed for locations of other monitoring sites
throughout the DWC to gain a better understanding of how the hydrodynamics
work through out this section of the river.  Charlie Kratzer suggests
talking to Rick Altman (USGS?) to gain his thinking on monitoring the river
here.

7. The D.O. data that Peggy and team collected this fall should be reviewed
against data collected by others (who?) who have monitored this section of
the river for other projects.

D.  Computer Modeling - Wangteng Tsai
1. Funding for Rough-cut Analysis and Next Steps
a. Are there any funds remaining from the $22,000 allocated to Systech to
use the model to assist in the rough-cut analysis?  If so, Fred and the
Technical Team would like to have some additional runs and parameters
explored.  Fred will check with Systech and work with them on this.

b. The group would like Systech to extend Figure 2 to include October,
November and as much of December as possible.

c. Run the model after putting in the continuous temperature data in key
locations (including R-5) in the low D.O. stretch in order to determine
better the model's ability to predict temperature levels.

d. Run the model with the new USEPA suggested theta value for temperature
and then compare this with the runs with the old theta value?  How
important of a difference occurs from this change?

2. Reaeration
a. How does reaeration work in the model?  What are the assumptions for the
operation of the Army Corps existing aerator?  No one in the meeting knew
how much aerators added to the amount of oxygen in solution under field
conditions.  The laboratory tests showed that the aerators could add 2000
pounds of O2 per day.  

b. Russ Brown has developed three different methodologies to test the
practical effectiveness of aerators. So far, no one has come forward with
funding to conduct studies on this.  This will be a high priority for
future TMDL research on implementation options.  It will likely be
important to modeling the contribution of the existing aerator on fall
water conditions and to accurately balance all the sources and sinks for
dissolved O2 in the DWC.

c. Fred Lee mentioned that a liquid oxygen aeration system is proving to be
quite effective in other environments.  It seems worthy for exploration as
an implementation option. 

3. Algal Load  
a. How does the model account for the chemical breakdown of algae over the
course of its decomposition? How much of it decomposes in what period of
time?  There is reason to believe that the algae breaks down completely and
within two weeks doesn't exert an oxygen demand.  During different stages
of decomposition different chemicals are produced with differing impacts on
dissolved oxygen.  What are the present assumptions incorporated in the
model?  How important is it for the model to include a more precise formula
for the decay exertion rate of different algae?

4. Terrestrial Organic Load
a. How does the model account for terrestrial organic load and how well is
this separated from algal load?  Also, studies indicate that terrestrial
organics decompose slower than algae and exert an oxygen demand over a
longer period of time.  Eventually, the model may need to assume different
percentages of terrestrial organic material entering the river from
different miles upstream and then calculate the oxygen demand they
contribute when they reach the DWC.  How will we determine whether this
level of sophistication is needed?

5. Biomarker and Tracer Research 
a. It may be that biomarkers and tracer research could help determine how
to create a formula that models the breakdown of algae from different
upstream sections of the river.  Tracers could help separate terrestrial
organic material from algal decomposition material.  Could it help
determine percentages of each in different sections of the river?

b. Elizabeth Kanwell (sp?) with the Virginia Institute for Marine Service
is working on tracer studies of terrestrial organics in the San Joaquin at
Mossdale.  Jim Chlorin (sp?) with (?) knows more about this CalFed grant.  

c. CalFed is also funding a DOC study in the SJR.  We need to be
coordinating with these projects. It would be good to know the hypotheses
they are testing and the methodologies they are using.  

6.  Continuous DO Monitoring Results
a. How well does the Systech model predict the D.O. deficits shown in this
past summer and fall monitoring data?  Is the D.O. simulation a good fit
with the observed data?  (There was disagreement on this among committee
members.)

b. Why is the model overpredicting D.O. in late August and September and
why doesn't the modeled D.O. levels drop off at the end of September like
they did in the river this year?

c. Does the time of day the river data was collected affect the D.O. model
prediction results?

d. There is concern that there are limits on how the D.O. data can be
interpreted because of the low number of data points.

7.  River Flow Data
a. Having accurate flow data for the San Joaquin below Mossdale and the
amount of water passing Channel Point is critical for quantifying the load
entering the Deep Water Channel.   Concerns and issues on flow data are
listed below.

b. The new UVM meter at Channel Point may not be accurate.  Has it ever
been verified?  (Someone needs to check with Rick Oltman (sp?)

c. Do we know the relationship between flow and water temperature?  Can we
correlate this to algal growth patterns?

d. RWCF flows and loads need to be separated out from river flows to get an
accurate estimate of the flow and load of the river upstream of the RWCF
outlet. 

8. Deep Water Channel Depths
a. If the DWC depth is lowered, how does this change the impact of tidal
flows on S.O.D.?  Does it stir up the sediment more or less? 

b. How do channel depths affect the sedimentation of material?  Would as
much settle if the channel was only 10 feet deep? Does it change the
location of where the sediment settles?

c. How does channel depth affect algal growth? Would more algae be alive
and adding net oxygen to the system if the channel was shallower?

9. Model Prediction of Algal Concentrations in 1999
a. How well does the model predict the actual algal concentrations that
were observed in 1999?

10. Complexity and Limitations of Modeling 
a. Alex H. raised concerns over how complex the natural system is and how
difficult it will be to model the large number of variables and gain a
clear understanding of the analysis.  
b. At the present time, the answer to this concern is that the technical
committee will attempt to diligently note the specific concerns about the
model's assumptions and other factors as they reviewed and utilized the
model in their analytical efforts.  


E.  Regression Analysis -  Erwin Van Nieuwenhuyse
1. Erwin presented a summary of various runs of a regression model he
developed to see how data gathered since 1984 (three stations) correlated
to low D.O. levels.  For a copy of his results and the spreadsheets
themselves, contact Erwin at .

2. Concerns were raised about serially correlated variables where factors
such as temperatures and flows or temperatures and algal mass are naturally
correlated and may not provide any clear explanation about how this is
really working in the field.  In response, Erwin will conduct additional
analysis on the importance of serially correlated variables.

F.  Sediment Oxygen Demand - Gary Litton
1. The general conclusion is that algae is decomposing and fueling S.O.D.
and significantly contributing to the Total Organic Carbon and Dissolved
Organic Carbon in the system, but there are doubts.

2. Studies show that as algae decompose, T.O.C. increases immediately but
then disappears.  What are the ramifications of this process on oxygen
demand in the system?  Could it be that algal impact on S.O.D. is not
significant and that other B.O.D is more important?

3. Terrestrial organic matter from farms and urban areas may be the biggest
contributor to S.O.D. in the Deep Water Channel because it takes a much
longer time for it to decompose.  We haven't separated out what are the
relative sources of S.O.D. in the Deep Water Channel.

4. Litton and his team have not quantified nor differentiated between
resuspension sediment rates and its demand on oxygen versus the roles of
the ongoing deposition of decaying matter coming in from upstream.  

5. What are all the causes of resuspension of sediments since resuspension
is suspected of exerting a higher oxygen demand than if the sediments
remained settled?  Besides ship traffic and tidal flows, what are the
causes of resuspension?  Does air and water temperature changes cause
resuspension?

6. It is suggested that S.O.D. tests be redone during slack (neap) tidal
periods in addition to the flood tide periods that were tested this last
year. 

G.  Other Issues
1.  The Role of Sediment
a. When does sediment enter the river?  Is it variable?  Can there be major
sediment events that could kill algae between Mossdale and Channel Point
that could add more oxygen demand to the system than normal?  This is a
hypothesis for why the August low dissolved oxygen event occurred. 

b. If sediment load is blocking light and causing algal death, could a
sediment trap and removal of sediment after Mossdale help light penetration?

2.  Low Dissolved Oxygen Levels in November and December
a. Previously it was thought that as water temperature dropped in these
months, low D.O. levels would end.  This year, researchers in the field
continue to record D.O. below 5 milligrams per liter.

b. Low flows and high export rates are a suspected major cause of the low
D.O. during these months.  This condition leads to long residency times in
the river and other conditions that appear to increase the factors that
lead to low D.O. levels.

3.  The late September Low D.O. Event
a. D.O. levels in the DWC dropped dramatically at the end of September.
The only thing different that seemed to occur at that time versus earlier
in the month is that the South Delta tidal barriers were removed.  Removal
of the barriers would change the flow throughout the area and may have
caused reverse flow conditions at Stockton.  

b. In addition, increased spring flows to meet VAMP outflow requirements
leaves less water available in the fall.  Were there fall "attraction
flows" released this year?  

c. Removal of the South Delta tidal barriers also may change biological
conditions throughout the area, which may impact D.O. levels.

4.   Integrating Solutions into Monitoring, Research and Modeling. 
a. The ultimate reason for doing all the studies and modeling is to develop
a management plan that will resolve the D.O. problem. What are the
manageable variables and are we investing enough in studying them, or are
we spending too much of our limited resources studying parts of the system
that cannot be managed?

b. For example, can the system's capacity to assimilate oxygen-demanding
material be increased so that less D.O. problems are caused?  Changes in
tidal barriers, increased flow through recirculation and other actions
could increase the system's assimilative capacity.

5.   Improve uniformity of data
a. Future monitoring and data collection should utilize a uniform standard
collection during the time of day, air temperature readings, and other
factors.	
b. Observation procedures need a unified process and procedure

6.  Tidal Impacts
1. Lower D.O. levels are recorded during high tide events and higher D.O.
levels on low tide events.  What mechanism is causing this relationship?  
2. Does high tide cause more algal death through decreased light or other
factors?  
3. Do high tides resuspend sediment and exert a greater  S.O.D. than low
tides?  

7.  Sediment Grain Sizes 
a. Vance Kennedy has information about the velocity of various sediment
grain sizes and how they would move downstream.  Contact him if you would
like more information on this.