**2. Background**

The San Joaquin River (SJR) drains approximately 8.7 million acres (4 million ha) of California's San Joaquin Valley including 1.4 million acres (0.64 million ha) of agricultural land (Figure 1). The San Joaquin River Basin (SJRB) watershed is bounded by the Sierra Nevada mountains on the east, the Coast Range mountains on the west, the Sacramento– San Joaquin Delta to the north, and the closed Tulare Lake Basin on the south. The Coast Range mountains are relatively recent in geologic history and formed of an uplifted seabed whose sedimentary constitution is naturally high in salinity including trace elements such as selenium, boron and molybdenum. [17–19]. Additional salt is imported to the basin from large state and federal water pumping facilities in the Sacramento–San Joaquin Delta. These facilities replace water supply that was diverted from the SJR to irrigate farmland in the southern part of the San Joaquin Valley in the 1960s [17] and constitute more than 47% of the salts imported to the basin. For this reason, as the main purveyor of irrigation water supply, the federal government is considered a stakeholder in actions to manage salinity impairments in the SJR.

Since the 1940s, mean annual salinity concentrations in the SJR measured at the Vernalis monitoring station, the most downstream station not impacted by tidal flows in the Delta, have more than doubled. West-side SJRB sources that include agricultural surface and subsurface drainage and surface drainage from seasonally managed wetlands that comprise the 140,000 acres (64,000 ha) Grasslands Ecological Area discharge through Mud and Salt Sloughs and accounted for more than 37% of the salt loading to the SJR for the period 2000–2009 (Figure 1). Several smaller, ephemeral streams including Hospital, Ingram, Del Puerto, Orestimba and Los Banos Creeks contribute an additional 30% to SJR salt loads [13]. The major tributaries to the SJR, the Stanislaus, Tuolumne, and Merced Rivers, drain the east side of the basin and are the major source of dilution flow and salt load assimilative capacity to the SJR (Figure 1).

Water quality data collected by the Central Valley Regional Water Quality Control Board (CVRWQCB) staff since 1985 indicate that the 30 day running average electrical conductivity (EC) water quality objectives of 1000 μS/cm in the non-irrigation season and 700 μS/cm in the irrigation season (1 April–31 August) have been routinely exceeded at the Vernalis compliance monitoring station, especially prior to 2005 [12,13]. The non-irrigation season salinity objective was exceeded 11 percent of the time and the irrigation season salinity objective was exceeded 49 percent of the time during the period 1986–1998 [13]. This rate of exceedance occurred even though releases were made from New Melones Reservoir on the Stanislaus River to help meet salinity objectives at Vernalis [12].

The SJR TMDL for salinity had several objectives, namely (a) to identify and quantify the sources of salt loading to the SJR; (b) determine the load reductions necessary to achieve attainment of applicable water quality objectives in order to protect beneficial uses of SJR water supply; and (c) to allocate salt loads to the various sources and source areas within the watershed which, once implemented, would result in attainment of applicable water quality objectives [13,14]. Figure 1 shows the seven source areas identified by the CVRWQCB that each were assigned annual and monthly salinity load objectives, modified to account for wet, normal, dry and critically dry water year classifications. However. realization of these objectives using a 10% low flow hydrology to account for critically low-flow conditions over a 73 year historical flow record, in lieu of the standard MOS, produced a TMDL where the base load allocations were overly conservative.

The TMDL already recognized a consumptive use allocation to account for irrigation evapotranspiration of applied water, a Delta Mendota Canal supply relaxation load for salt imported with water supply deliveries to the west side of the basin, a SJR supply water relaxation for salts diverted from the SJR and an allocation to the federal agency for actions related to mitigation of salts imported by the agency in irrigation water supply. The USBR was assigned responsibility for 47 percent of the salt load discharged to the SJR [13].

Analysis conducted by CVRWQCB staff showed that stakeholder adherence to these salt load limits would result in salt accumulation in the watershed and long term of both degradation of ground and surface waters. Continuation of existing drainage practices could result in average annual fines of over \$300,000 in each of the subareas (Table 1) assuming a fine schedule of \$5000 per day for each month the load allocation for each subarea was exceeded [20]. These fines would be borne largely by agricultural water district stakeholders, some of whom are those adversely impacted by elevated EC in the SJR primarily along Reach 83 (Figure 1). Agriculture is the primary beneficial use impaired by salinity in the SJR Basin recognized in the SJR Basin plan [13,14]. To overcome the constraints imposed by the conservative nature of the strict TMDL formulation, the CVRWQCB made provision for an additional real-time salt load allocation in lieu of the fixed base load allocation to maximize salt export from the LSJR Basin while still meeting water quality objectives [14]. The real-time load allocation would apply any time salt load assimilative capacity was available in the SJR.

**Figure 1.** Major subareas within the SJR Basin that drain to the SJR as defined in the salinity TMDL [13]. Reach 83 shown in the figure is the reach for which water quality (salinity) is regulated through the recognition of three compliance monitoring stations at Crows Landing, Maze Road Bridge and Vernalis. The most salient feature of the SJR Basin is that drainage from sources to the west of the SJR are elevated in salinity by virtue of native salts in alluvial sediments deposited from the coastal range mountains west of the Valley floor and the importation of irrigation water supply from the Sacramento-San Joaquin Delta that is also salt impacted. Tributary inflow from land areas to the east of the SJR are of high quality, derived from snowmelt from the Sierra Nevada mountains. Real-time management is essentially a scheduling activity—coordinating salt load assimilative capacity consumed by west-side saline drainage with salt load assimilative capacity supplied by east-side reservoir releases along the major tributaries.


**Table 1.** Hypothetical SJR daily salt discharge exceedance fees by subarea (10-year period 2001–2012) using an assumed \$5000/day fine for exceedance of the 30-day running average mean EC objective [20].
