*3.2. Analysis of Exceedance Frequency of San Joaquin River Salinity Objectives*

The first step in assessing salinity management options and developing policy for the trading of salt load credits was to look at the exceedance frequency at the three compliance monitoring sites. Given the changes in the San Joaquin Basin hydrology over the past fifty years, in part due to the hydrologic variability induced by a warming planet and climate change, only the past decade of the San Joaquin River hydrology was included in this analysis. A pattern is emerging in California of more persistent back-to-back droughts punctuated by years of abnormally wet weather (State of California [35]).

Table 1 presents a schedule of potential annual average penalties (2001–2012) that could have been assessed for exceedances of salinity objectives at Vernalis under the salinity TMDL, assuming a hypothetical penalty of USD 5000/day for each monthly overage [28]. Subareas include Northwest side (NWS), Grasslands (GL), Upstream San Joaquin River (SJR), and East Valley Floor (EVF).

In December 2018 the Environmental Protection Agency approved a Regional Water Board Basin Plan amendment that established upstream objectives at the Maze and Crows Landing monitoring locations on the San Joaquin River. These objectives were ostensibly to protect the water quality of riparian diversions to westside San Joaquin River irrigation districts. The objectives of 1550 uS/cm apply year-round at both monitoring stations and considered the field crops and orchards farmed adjacent to this reach of the river. Figures 3 and 4 show the 30-day running average EC at the Maze and Crows Landing compliance monitoring stations for the period 1 October 1995 through 1 September 2013. At Maze Road some of the highest EC values occurred in below-normal years as opposed to dry and critically dry years, although, all the data appear well below the 1550 uS/cm concentration objective. Maze Road is downstream of the Tuolumne River which appears to provide adequate dilution flow year-round. On the other hand, the Crows Landing site did show exceedances of the 1550 uS/cm objective during April for all three water year types (below normal, dry, and critically dry). Since the Vernalis compliance monitoring station is downstream of the Stanislaus River and was obligated to meet the winter 1000 uS/cm objective and 700 uS/cm objective through controlled releases by the USBR through their New Melones Reservoir operation, the incidence of exceedance was largely eliminated at this site [33,34].

**Figure 3.** Maze Road Historical 30-day Running Average EC by Water Year Type [36].

An analysis of the 30-day running average EC was subsequently conducted for all three compliance monitoring stations using more decent data for a 21-year period between 2000 and 2021. The same logic was applied as in the prior Regional Water Board compliance penalty analysis [35], although in this instance a second policy was introduced that imposed a fine of USD 10 per ton of salt. This fine schedule was chosen ostensibly to be a round number that produced an outcome of similar magnitude to the first policy when the 30-day running average monthly objective was exceeded. Figure 5 is a bar chart showing the frequency (number of days) that the 30-day running average EC was exceeded at each of the compliance monitoring stations. In Tables 2 and 3 the potential fines were compared for the two policies for each month of the 21-year period. Note that this is a slight variation of the prior Regional Water Board policy, which imposed a penalty for all days of the month anytime the 30-day running average EC was exceeded in any month. With the use of the WARMF forecasting model and decision support system, calculation of the 30-day running average has become routine and provided a more equitable policy outcome. With better online real-time access to estimated salt load from each of the seven subareas the response time for remedial actions on the river was reduced. However, an institutional mechanism for deciding real-time actions has still to be ratified by designated resource managers for each of the seven subareas contributing salt load to the San Joaquin River.

**Figure 4.** Crows Landing Historical 30-day Running Average EC by Water Year Type [36].

The summary provided in Tables 2 and 3 shows that the Crows Landing station is largely controlling salt management in the San Joaquin River. Hence, actions to achieve compliance with the Crows Landing objectives need to be implemented in the three subareas upstream of this compliance monitoring site. This would include the Grasslands, San Joaquin River Above Salt Slough and Merced River catchment subareas (Figure 2). The Grasslands subarea comprises agricultural, wetland, and municipal stakeholders and a cost-effective equitable response would need to be developed among these entities. The majority of exceedances at the Crows Landing compliance monitoring station occurred in the months of March–May (Figure 4), which coincided with the wetland drawdown period when irrigated agriculture in the subarea was also providing pre-irrigation to field crops and orchards. Although the last 20 years have seen a significant move to drip irrigation, more water conserving technologies and selenium management practices have eliminated a major source of salt load from the subarea. Subsurface tile drainage is now diverted to a dedicated 6000+ acres of reuse area, thus, any response would be expected to include actions from all three entities. Managed seasonal wetlands in the Grasslands subarea are constrained by the fact that any significant delay in wetland drainage from the 160 private duck clubs and state and federal refuge wetland complexes can change the germination success of high-value grasses potentially leading to lower value habitat for the overwintering waterfowl that rely on this resource [37,38]. Irrigated agriculture may need to invest in additional temporary storage ponds in areas free of selenium in shallow groundwater (selenium is a potential toxin when drainage concentrations exceed 5 ppb) or automation of sump pumps and new drainage conveyance plumbing to facilitate salt

management through reuse and drainage recirculation. Municipal discharge of salts in the Grassland sub-basin is minimal with most ponded water being eliminated through seepage to groundwater. Municipal wastewater facilities may own storage ponds that might be usable and temporary storage facilities to reduce salt loading from the Grassland subarea. The potential for this cooperative and coordinated salt management strategy is unknown at this time. In the Merced River catchment subarea, the salt load contribution to the river is dominated by the reservoir releases from the McSwain and New Exchequer Dams and irrigation return flows into the Merced River. The Merced National Wildlife refuge contributes an insignificant return flow given its reliance on groundwater as the water supply source. The subarea south of Salt Slough is bottomland in the Valley trough and contributes to the San Joaquin River through groundwater seepage. Reservoir releases from Friant Dam can be diverted into the subarea through riparian pumping. Seepage may occur from the river into the subarea in response to local groundwater pumping.

**Figure 5.** Exceedance frequency of 30-day running average EC at all three compliance monitoring stations of the San Joaquin River for 21 years: 2000–2021.


**Table 2.** Historical accounting on salt load exceedance, days of exceedance, monthly fees, and fine for salt load exceedance 2001–2021 at Crows Landing [36].


**Table 2.** *Cont.*

Note: Total cost in nominal dollars. Values elaborated by authors, based on data in [36].

**Table 3.** Historical accounting on salt load exceedance, days of exceedance, monthly fees, and fine for salt load exceedance 2001–2021 at Maze Road [36].


Notes: (1) Exceedence during the analyzed period occurred only in January and July 2015. (2) Total cost in nominal US dollars. Values elaborated by authors, based on data in [36].
