SAN JOAQUIN RIVER Dissolved Oxygen Total Maximum Daily Load Stakeholder Process

San Joaquin River Dissolved Oxygen TMDL
Technical Committee Meeting  - DRAFT Notes
 December 13, 2000

Attending: Attending: Russ Brown (JSA), Carl Chen (Systech), Chris 
Foe (REWQCB), Dan Hinrichs (DJH Engineering/City of Modesto), Bill 
Johnston (Modesto ID), Charlie Kratzer (USGS), G. Fred Lee (chair), 
Peggy Lehman (DWR), Bob Murdoch (Stockton), Tom Quasebarth 
(CDM), Nigel Quinn (LBNL/USBR), Rich Stowell (Farm Bureau), 
William Stringfellow (LBNL), Alice Tulloch (Tulloch Eng), Kevin Wolf 
(facilitator and notes 530-758-4211, kjwolf@dcn.davis.ca.us)

Next Technical Committee Meetings:
January 10, 9 am - noon,  Location:  To be announced. 
 
Handouts
1. “Discriminating Wetland and Agricultural Carbon and Nutrient Loads 
to Mud and Salt Slough”, An Executive Summary of a Proposal for 
Directed Action Funding.  William Stringfellow

A.  Computer Modeling of Loads Upstream of Vernalis
1. The goal of the upstream model is to accurately predict algal, carbon 
and nutrient loads at Vernalis under different flow levels and different 
weather conditions.

2. The model will utilize the best available data of loads and flows 
entering the main river from the tributaries and groundwater.  It will 
also incorporate diversions from the river so that upstream loads can 
be appropriately reduced based on the percent that is diverted before 
reaching Vernalis.  The mass balance of the load accretions minus 
diversions should equal the measurements made at Vernalis.  

3. Algal species and growth information 
a. Different algal species have different growth rate dynamics and 
potential impacts on downstream oxygen demand..  Peggy Lehman 
reports that algal populations in the river can change dramatically in a 
short period of time.  Algal species and dynamics may be important to 
predicting the episodic low dissolved oxygen crashes that occur but 
presently are not showing up in the model runs.  Diversions from the 
river may also be responsible.  Peggy and Carl Chen will review her 
proposal for algal species work above Vernalis to help make sure the 
information she generates can be used by the computer model. 

b. Peggy will review the information available on algal growth rates for 
species important to the San Joaquin and recommend whether 
additional studies should be conducted so that good predictive 
equations for the growth dynamics can be used in the computer 
model. 

c. There appears to be more respiration occurring in the river than is 
showing up in BOD studies.  This could be the result of paraphyton 
on the river bottom or by clams, though it is not thought to be 
important by knowledgeable TAC members. Peggy will review the 
available information and recommend whether additional studies on 
these two factors should be included in the 2001 Directed Action 
proposal.

d. Algal growth seems to be only limited by light (solar radiation) 
intensity and availability as nutrients are not limited.  Light intensity 
varies with the weather, which is incorporated into the computer 
model.  The bigger impact on light availability is associated with 
sediment loads and the size and types of sediment in the water 
column.  Peggy believes that there is sufficient information on light 
availability from turbidity monitoring and Secchi depth measurements 
being conducted as part of the algal sampling program.   If the algal 
growth dynamics do not function as predicted based on solar radiation 
availability, then new studies should be conducted in 2002. Presently, 
the committee feels that there is sufficient information in this area do 
not think additional studies are needed in 2001.  

e. Zooplankton populations may be impacting algal populations and 
growth rates.  The peer reviewers want zooplankton studies to occur 
in the DWSC.  Peggy will develop a proposal for doing zooplankton 
studies.

4. Continuous monitoring in the river above Vernalis.
a. The committee determined that another continuous monitoring station 
should be placed upstream of Vernalis, most likely at Crow’s 
Landing.  This monitoring station should collect data on turbidity, 
light intensity, N, P, VSS, EC, TOC, BOD, chlorophyll, and 
pheophyton. 

b. Peggy will work with Nigel Quinn to determine the costs and efficacy 
of this type of monitoring at Crow’s Landing and develop a proposal 
for Directed Action funding. 

c. Chris Foe proposed and the TAC agreed to allocate funds in the 
proposal for a third monitoring site in addition to Vernalis and 
Crow’s landing.  The location will not be set until after the strawman 
analysis is completed. 

5. Additional Monitoring at Vernalis
a. Continuous phlorometer and dissolved oxygen data should be 
collected with other data at the Vernalis station.  Peggy will develop a 
proposal to do this. 

b. Nigel will check to see if the USBR building at Vernalis would be 
available for the monitoring work.  Vernalis is not an easy location 
from which to monitoring and the USBR property could be very 
helpful. 

6. Upstream of Vernalis sampling by the USGS
a. With the 2000 CALFED grant, USGS was able to do bimonthly 
monitoring at four locations in the river upstream of Vernalis from 
July through October.  The Technical Committee wants them to 
continue at least at this level from June through November, and 
would prefer that they increase the number of times they sample 
to once per week, if possible.  

b. The USGS sampling is more expensive than other sampling efforts 
because they use an integrated sampling technique across the width 
and depth of the river at each location.  This helps ensure that the 
sample is more representative of the river at the location and moment 
in time than a simple grab sample.  Additional integrated sampling 
that corresponds to the grab sampling being done at the same time and 
location will help in correlate the data and could provide a means to 
improve the historic grab sampling data. Evidence from 2000 shows 
that there is a 20-25% difference between the two techniques.   It was 
debated but not concluded whether an additional year’s worth of 
integrated sampling would provide a statistically significant 
relationship with grab samples and whether this was more valuable 
than doing more grab samples.  Charlie Kratzer will provide a more 
detailed proposal on the sampling program with the two different 
techniques.   

c. Suspended organic carbon data differs between the UCD studies and 
the USGS studies and seems to be the result of the grab sample 
technique versus the integrated sample technique.  Continued 
integrated sampling next year may help correlate the two different 
results. 

d. The USGS proposal will include sampling at eight tributary sites just 
upstream of the main river in 2001.

7. Groundwater inflow to the river
a. There is general agreement that there is inadequate information about 
the amount of load and flow being contributed to the river from 
groundwater sources.  When river flows are low, estimates for 
groundwater inflow range from 2-8 cfs per river mile.  The nutrient 
load associated with this flow is unknown.  The origin of this flow is 
also unknown.  Sometimes groundwater from one side of the river can 
enter the groundwater supplies on the opposite shore.  Groundwater 
inflow impacts can be especially important during low flow years.  
Some stakeholders that may be allocated load reduction requirements 
do not want to have this source of loads not be attributed to a 
responsible party because it was thought to be too expensive to do the 
necessary research.  If this load is not allocated, their share and 
potential costs will rise.

b. It is agreed that more accurate measurements of surface water inflow 
and diversion will help in determining the inflow from groundwater. 
This would not though resolve the issue about how much load is 
coming neither from the groundwater nor from where the 
groundwater is originating.  It would just make the mass balance of 
flows more accurate. 

c. Charlie Kratzer and the USGS were asked to develop a psiometer 
study plan for assessing groundwater inflow and outflow along the 
entire length of the San Joaquin River.  This study would also provide 
information on the quality of key constituents of the groundwater.  It 
would evaluate groundwater flow amount and direction by assessing 
the slope of the neighboring groundwater supplies.  It will utilize the 
historic data that USGS collected and possibly even using the existing 
psiometers that are in the river banks at Crow’s Landing and 
Patterson. 

d. Alice Tulloch was asked to develop a proposal to “mine” historic 
groundwater information and data that could be useful to determining 
the amounts and sources of groundwater inflow into the river.  Some 
of the potential sources of this information include cities discharging 
effluent to land, dairies and feedlot operators, UC Coop Extension 
(Thomas Harter), the USBR, DWR and others.

8.  Diversions from and inflows to the river
a. Gaining an accurate analysis of inflows and diversions to and from 
the river will be important to the computer model’s ability to 
accurately predict low dissolved oxygen levels in the lower river.  
Presently the model will utilize the SJRRIO/DSM2 model results that 
DWR is developing.   Their model is the most sophisticated one 
available but it still does not utilize real inflow and diversion data 
because it is not available.  Diversions and tail water return is not 
monitored nor metered.  

b. The USGS started collecting diversion and return flow data from 
Oristemba Creek in 2000.  They do not though collect water quality 
data at this location.

c. Nigel Quinn will develop a proposal for querying water districts and 
other diverters along the mainstem river upstream of Vernalis to see if 
they have any data that they would share for our modeling work.  

d. Nigel will also ask Patterson and El Sol, the two other major diverters 
if they would do the same level of monitoring that is done on 
Orestimba Creek. 

e. The TAC determined that more dye studies would not provide 
sufficiently valuable enough information to justify including in the 
grant. If though there isn’t any way to get more information about 
diversion rates and locations, this may be needed.

f. Location of diverters is not fully known.  The Regional Board 
developed a database of known locations in the late 1980s but it is not 
thought to be fully accurate at the present time. The RB is 
overwhelmed with work and would prefer that someone else do this 
study.  (Who said they would develop the proposal?)

9. Mud and Salt Slough and Grasslands Monitoring
a. The strawman analysis using USGS data from the 1980s shows that 
this location may be a major provider of problematic loads to the 
river.  New data from 2000 studies will help determine if this 
continues.  Given their distance from the DWSC and the long time in 
which their nutrients can promote algal growth, it is likely that they 
will continue to be identified as a major load contributor.  

b. There is little nutrient, carbon or BOD data available from this area.  
There is an increasing amount of good information being developed 
about salt loading.  The TAC requested that Nigel Quinn develop a 
proposal to add on the nutrient and BOD/TOC monitoring to the 
existing monitoring that he is doing in this location.  Likely this will 
be needed in at least two locations – one to evaluate the impacts of 
wetlands, the other the impacts of agriculture.  (See “Discriminating 
Wetland and Agricultural Carbon and Nutrient Loads in Mud and Salt 
Slough.)

c. Los Banos Creek may also be an important source of nutrients and 
carbon.  The city of Los Banos (and the City of Justine?) discharges 
effluent to this creek.  Ag and wetland runoff also enters the creek.  It 
was not determined whether to pursue monitoring of this location in 
the 2001 proposal.  We can determine each cities discharge rates and 
qualities through their NPDES discharge reporting to the Regional 
Board.

d. Fred Lee is organizing a tour in January of the area with Nigel. 
Anyone interested should contact him.

10.  Data needed downstream of Vernalis
a. Inflow and diversion data is needed for the river between Channel 
Point and Vernalis in order to determine how much of the loads from 
upstream are affecting the dissolved oxygen levels in the DWSC.  
Little data has been identified for this area besides from the cities, at 
Mossdale and from French Camp Slough.  One estimate is that there 
are 25 discharges and 50 diverters in this section of the river.

b. Alex Hildebrand will be asked to help develop a proposal to find any 
historic data from the westside of the river and to determine the 
amount of diversions and inflows along this stretch. This is 
predominantly in the South Delta Water Districts area.   It is unknown 
who will help carry out the work needed to do this work.  

c. Nigel Quinn will develop a proposal for investigating historic data 
available from the eastside of the river.  

11. South Delta Barrier Operations
a. The Technical Committee hopes that CALFED will fund studies 
needed to determine the effectiveness and impacts of operational 
scenarios of the south delta barriers that could benefit flows in the 
lower San Joaquin River.  

b. Peggy Lehman said that a meeting is occurring on December 14 with 
DWR at which this issue will be discussed.  Ideally, DWR will 
include the scenario operations in their modeling runs and analysis.  
Peggy will report back on what DWR is thinking and what our best 
options are.

c. The TAC requested that a TAC member develop a proposal to liaison 
with DWR’s modeling team in coordinating our modeling needs so 
that they are met as best as possible when DWR does its work.  Carl 
Chen was asked and agreed to develop a proposal for fulfilling this 
role. 
  
12. Grant Administration
a. Fresno State is unable to reduce its grant administration charge of 
15%.  

b. Jones and Stokes had an administrative charge of around 7% and 
thus was asked to provide a more detailed proposal.  The state and 
federal partners in the grant stated that their agencies would have 
trouble receiving funding through a consulting firm.  Peggy, Charlie 
and Nigel were asked if they would check with their administration 
about receiving the grants directly from CALFED but having JSA do 
the administrative reporting parts of the grant.  It is hoped that these 
agencies can find a way to make this work. 

13. WARMF Model
a. Carl Chen raised the issue that the WARMF model could be a 
valuable tool in helping estimate the loads coming into the river from 
the subwatersheds.  By using fertilizer application rates, soil types, 
crops and dairy information, water application rates and other GIS 
layers, the model can estimate inflows into the SJR.  This could help 
correlate and calibrate other monitoring data.  This could be 
especially useful in the Mud, Salt Slough and Grasslands area.  

b. The TAC did not make a decision on this but, in general thought that 
it was a good proposal to make for Prop. 13 and other funding sources 
as WARMF is predominantly design to be an implementation 
decision support tool.

14.  Miscellaneous
a. Data Availability
i. Important data should be made available via the Interagency 
Ecological Program’s website with the help of DWR.  Karl Jacobs is 
in charge of this effort.  Funds have been made available to the 
project from the year 2000 CALFED grant.

ii.  Peggy Lehman will find out from Karl who is contributing data 
important to the dissolved oxygen and will post that list to the email 
listserv.  

iii.  Carl Chen will review his model and provide a list of the data sources 
he presently has available to him.  He will post this to the listserv.  
Everyone is requested to review this information and see if there are 
other sources of data that also could be used.   

b.  Data Accuracy
i.  There is concern that different labs may be analyzing the data 
differently and providing different results.  There may also be 
differences in sampling techniques.  If this is true, a correlation can be 
done to correct the differences.  

ii.  Fred Lee is attempting to find out what different data providers are 
collecting, the methods they are using, and how they are doing QA/QC.