**3. Model Testing**

*3.1. Application to Water Quality Issues in the San Joaquin River*

Salinity loads to the San Joaquin River (SJR), the receiving water body for agricultural drainage in the San Joaquin Basin, are regulated by the State of California through the Central Valley Regional (Water Quality Control) Board. A TMDL was developed that set load limits for each subarea [33,34]. The TMDL for each of the seven subareas (Figure 2) was largely based on basin hydrography, and existing water district and jurisdictional boundaries. Four of these subareas (Northwest Side, East Valley Floor, Grasslands, and San Joaquin River Above Salt Slough) are located on the valley floor, and drainage from these subareas is dominated by agricultural and managed wetland decision-makers. The other three subareas are watersheds serving three major east-side tributaries to the SJR, namely the Stanislaus, Tuolumne, and Merced rivers. Given the institutional history and management functions within the basin, these seven subareas are the most logical management units and any possible future trade in salinity load permits would initially occur between these entities.

The load allocations under the TMDL ended up being overly restrictive, following the typical TMDL development methodology and would have resulted in potential annual fines in the order of USD 300,000 per subarea based on a 9-year average of salt loads. Load allocations were based on a design flow hydrology representing the lowest 10% of monthly flows. An additional safety factor was applied to the allowable monthly salt loads which further reduced stakeholder ability to meet objectives. The Regional Board adopted a real-time concentration-based schema to substitute for the TMDL salt load based approach which allowed greater use of the river's assimilative capacity. Salinity management in the San Joaquin River Basin is complex, involving agricultural, wetlands, and municipal stakeholders within the basin. Being cognizant of this complexity and the difficulty of building coalitions among entities that had little history of working cooperatively, the Regional Water Board named the alternative approach to TMDL implementation "realtime salinity management". The current Basin Water Quality Control Plan for the San Joaquin Basin lays out the general requirements for a Board-approved Real-Time Salinity Management Program:

1. The program is a basin-wide program requiring all stakeholders discharging to the SJR to be signatories and active participants.


**Figure 2.** Map of the various San Joaquin River Basin contributing subareas as defined in the 2002 TMDL Regulation Plan: Northwest Side (NWS), Grasslands Agriculture (GRA), East Valley Floor (EVF), Merced River (MER), Stanislaus River (STL), Tuolumne River (TLU), and San Joaquin River above Salt Slough (SJR). Note: the eight red triangles in the Figure that are indicated in the legend by numbers 1–8 are the locations of the flow and salinity load monitoring stations. Source: [33,34].

Salinity concentration objectives for compliance monitoring stations at Crows Landing bridge, Maze Road bridge and Vernalis were set as 30-day running averages of EC. For Vernalis these salinity concentration objectives were a winter objective of 1000 uS/cm and a summer objective of 700 uS/cm. The summer irrigation season salinity objective was considered protective of irrigation agriculture and salt-sensitive crops. A year-round salinity objective of 1550 uS/cm was later set for compliance monitoring stations at Maze Road Bridge and Crows Landing Bridge, set to be protective riparian diversions used primarily on orchards in the river reach between Crows Landing Bridge and Maze Road Bridge.

Using a water quality simulation model as a real-time decision support tool, two-week forecasts of the 30-day running average salt load assimilative capacity were made routinely for the San Joaquin River at each compliance monitoring station. The model provides information on the salt loads from each of the seven subareas and computes the excess load that must be removed from the system by one or a number of salinity management options that can adjust the scheduling of salt load discharge into the river, including: temporary storage of these salt loads in ponds; shutting off discharge from agricultural drainage sump pumps into drainage conveyances for periods of time; recirculating or reusing return flows of high salinity; and/or providing dilution flows from eastside tributary reservoirs to lower ambient salt concentration in the river to meet salinity concentration objectives. To illustrate the potential use of assimilative capacity, the USBR calculated the available daily salt load assimilative capacity in 2008, a year when violations of the salinity objective were still common. During 2008, the SJR salt load assimilative capacity was available on 246 days of the year (conservatively estimated when the SJR salinity was less than 85 percent of the salinity objective) for a total of around 115,000 tons of salt (calculated on a daily basis). The salt load assimilative capacity of the SJR was exceeded for 119 days.

A "strawman" allocation policy was developed as part of an analysis by Regional Board staff in 2015, to demonstrate the potential fines that might have occurred under the published TMDL using a suggested daily fine of US\$5000 per day for each overage of the EC objectives. The cultivated area in each subarea was the means by which the total fine was distributed among subareas and the stakeholders within each subarea. During periods when salt load assimilative capacity in the San Joaquin River was exceeded, stakeholders within each subarea were obliged to provide a collective response to salinity objective exceedances. Stakeholders in one subarea could engage in voluntary agreements with stakeholders in other subareas through their representatives to trade individual subarea salinity load exceedances for a number of management actions to be deployed in the other subregions. The schema that was developed (Table 1) made clear the merits of a collaborative and coordinated real-time water quality management program, even though the ability of stakeholders to develop the partnerships required to realize the benefits of the proposed alternative regulatory policy remained untested. One concession made by the Regional Board was that in critically dry years, when the option was typically foreclosed of releasing dilution flows from tributary reservoirs to help meet the three salinity concentration objectives in the San Joaquin River, was that all three salinity concentration compliance objectives would be waived.


**Table 1.** Potential Salt Discharge Load Exceedance Fees by subarea (2001–2012), ref. [35].

Note: <sup>a</sup> VAMP stands for Vernalis Adaptive Management Program. These were programmatic reservoir releases for fish migration that occurred each year from 15 April to 15 May. Values in the table are elaborated by the authors, based on data in [35].
