Managing Water and Crops with Groundwater Salinity – A growing menace

by Yiqing “Gracie” Yao and Jay Lund

Salinity is an eventual threat to agriculture and groundwater sustainability in parts of California, and other irrigated parts of the world. Irrigation, lower groundwater levels, and natural conditions have dramatically increased groundwater salinity in parts of California over the last 150 years (Hansen et al. 2018). Nearly two million tons of salt accumulates per year in the San Joaquin Valley (CV-SALTS), where 250,000 acres of irrigated land have been fallowed, 1.5 million acres are potentially salt-impaired (Great Valley Center 2005), with $1.2 – $2.2 billion/year losses by 2030 (Howitt et al. 2009) without management. Managing groundwater with salinity can differ fundamentally from conjunctive water management without salinity, which was summarized in a previous blog post.

Salts accumulate in soils and shallow groundwater in arid and semi-arid areas because higher evapotranspiration rates and lower precipitation leave salt in the soil, requiring more irrigation water (also containing salts) to leach soil salinity to groundwater or drainage systems. However, without drainage from a basin, as occurs when low groundwater tables prevent salt drainage to rivers, soil salinity collects in underlying aquifers and groundwater salinity can only increase with time (Pauloo and Fogg 2021). 

With every pumping-and-recharge cycle, the groundwater becomes saltier. This is common in western parts of California’s San Joaquin Valley (Hansen et al 2018). Salts in soil and irrigation water reduce crop yield and quality, with foreseeable salinization and agricultural losses for the San Joaquin Valley.

Groundwater salinity and conjunctive use of surface water and groundwater

A recently-completed hydro-economic optimization model examines conjunctive water use and cropping patterns for extensive irrigated agriculture with increasingly saline groundwater (Yao 2020). It models crop planting and water management to maximize profits over a 10-year period with surface water availability varying from dry to wet years (event 1 = driest to event 5 = wettest), considering salinity’s harm to crop yields. The modeling was applied for conditions similar to the western San Joaquin Valley. For simplification, the model assumes blended irrigation water to reduce salinity effects on crop yields. 

Model results show that conjunctive use with more saline groundwater differs fundamentally from conjunctive use without salinity (Figure 1). With little groundwater salinity, semi-arid agricultural regions tend to pump more groundwater in drier years to supplement scarcer surface water. As groundwater become saline enough to reduce crop yields, economically optimal conjunctive use shifts to pumping less in drier years and pumping more in wetter years (Figure 1), when surface water can dilute more saline groundwater.

Figure 1. More saline groundwater fundamentally shifts groundwater operations from pumping more in dry years to pumping more in wetter years, when more saline groundwater can be diluted with fresher surface water (Yao 2020), while maintaining groundwater storage.

Cropping patterns and crop water use with groundwater salinity

Figure 2 shows water use for perennial and annual crops over the range of dry to wet years for different groundwater salinities.

At low groundwater salinities, more perennial crop acres are grown. As groundwater salinity rises to the salt tolerance of the perennial crop, groundwater’s ability to furnish useable water for dry years to grow perennial crops diminishes rapidly, because driest years have the least surface water to blend with more saline groundwater. Otherwise, perennial crop yields decrease uneconomically. Reduced pumping in drier years substantially reduces a region’s ability to support perennial crops and can eliminate annual crops with lower value in dry years.

To maintain groundwater levels, groundwater pumping increases in wetter years when more surface water is available to dilute more saline groundwater, but the additional pumping is used to grow lower-value annual crops. With higher groundwater salinities, annual crop acreage in wetter years is limited by irrigation water salinity. If all available water (surface water plus groundwater) is used to grow crops in the wettest years, the additional deep percolation forces more groundwater pumping to avoid waterlogging. More pumping increases salinity in irrigation water as the amount of surface water is fixed for each water year type, while more saline irrigation water reduces crop yields. Therefore, fewer annual crops are planted, and excess water must be disposed from the basin (brown arrows in Figure 2). 

Figure 2. Relationship between crop water requirement and irrigation with no overdraft. Brown arrows in the wettest year for high salinity cases are unused water externally drained.

Economic value of water with groundwater salinity

Table 1 summarizes how groundwater salinity affects the economic value of surface water and groundwater. When groundwater salinity is low, groundwater has greater value, as it can help support more perennial crops in dry years (when surface water is unavailable). With higher groundwater salinity, this drought buffering is unavailable and becomes a cost to agriculture, as pumping makes irrigation water too salty for perennial crops, reducing both crop yield and profit. At the two highest groundwater salinities, groundwater is so undesirable (in this model) that saline groundwater is pumped only for discharge outside the basin to avoid waterlogging (imposing pumping and disposal costs without profit).

Table 1. Summary of economic values of water ($/AF) in different hydrologic events with different groundwater salinities for a no-overdraft goal.

Salination of groundwater makes surface water more economically valuable, as it makes useable water scarcer overall. Surface water availability in the driest years limits the extent of profitable perennial crops, making farmers willing to pay more for this water (roughly the cost of desalted water in this case). The range of economic values for surface water widens across years as groundwater becomes more saline. For low salinities, the availability of fresh groundwater dampens water price variation across years. But with more saline groundwater, the variability in surface water’s economic value expands, rising for dry years and declining, eventually to zero, for wetter years. 

A drier climate further increases the value of surface water in the driest year and reduces agricultural profit. When groundwater salinity is low, overall usable dry-year water scarcity is less, and we value groundwater more. However, if groundwater salinity is too high, groundwater reduces agricultural profitability for drier climates.

Artificial recharge in the context of groundwater salinity

From Figure 2, high groundwater salinity leads to externally discharging water in the wettest years to physically remove both salt and excess recharge (deep percolation) from the basin. In such cases, raising water tables can be more profitable (if waterlogging is not an issue), by reducing need to pump (and waste) saline groundwater, having the same acreages of perennial crops with more lower-value annual crops in wettest years (Figure 3) as no pumping occurs in these years and irrigation water salinity is not a concern anymore. Artificial recharge of fresh surface water also can reduce groundwater salinity, at least locally, to make more groundwater fresher for dry year use in the future. Starting artificial recharge with fresh surface water early can slow groundwater salination and reduce its effects on water and crop management.

Figure 3. With high groundwater salinity (Cgw = 6,000 mg/L), mild aquifer recovery can be more profitable. Also, artificial recharge somewhat dampens the difference in surface water variability in wetter years.

Unlike pumping decisions, which are limited by irrigation water salinity, artificial recharge occurs in wetter years when perennial crops are irrigated only by fresh surface water. Therefore, artificial recharge still serves the original function of conjunctive use to dampen surface water variability. Annual crop acreage in years without artificial recharge should never exceed annual crop acreage in years with artificial recharge, and annual crop acreage is the same across years with artificial recharge (Figure 3).


For parts of California where salts accumulate in groundwater without drainage from the basin (mostly western San Joaquin Valley), growing groundwater salinity seems destined to bring a somber future for agriculture. Here eventually, salinizing groundwater will have diminishing ability to serve as a drought reservoir for drier years, and perennial crop acreage will become limited by surface water available in drier years, with greater annual crop acreage fluctuations. Profitable agriculture will still exist, but will be smaller, less profitable, and more variable across wetter and drier years. Though costly, earlier restoration of the aquifer levels, with reduced pumping and increases surface water recharge, can slow salination of groundwater and prolong the value of the aquifer for agriculture.

Many variants of this problem and solutions can be explored; some will be helpful.  Desalting of groundwater for irrigation will continue to be intensely explored and advocated, but will always remain expensive and unsuitable for lower-valued crops.  There is no cheap and permanent escape from the Valley’s water and salt balance problems.

Salinity accumulation is an ancient menace for irrigated agriculture, from ancient Mesopotamia to the present day. After groundwater overdraft is tamed, groundwater salinity will drive changes in groundwater management and overlying agriculture. 

Dr. Gracie Yao recently completed her PhD in Civil and Environmental Engineering at the University of California – Davis.  Jay Lund is a Professor of Civil and Environmental Engineering at the University of California – Davis

Further Reading

Yao, Y. and J. Lund (2021), Managing Groundwater Overdraft – Combining Crop and Water Decisions (without salinity),, January 17, 2021

Yao, “Gracie” Yiqing (2020), Managing Groundwater for Agriculture, with Hydrologic Uncertainty and Salinity, PhD dissertation, Department of Civil and Environmental Engineering, University of California – Davis.

Dogan, M., I. Buck, J. Medellín-Azuara, J. Lund (2019). Statewide Effects of Ending Long-Term Groundwater Overdraft in California, Journal of Water Resources Planning and Management, Vol 149, No. 9, September.

Escriva-Bou, A., R. Hui, S. Maples, J. Medellín-Azuara, T. Harter, and J. Lund (2020), Planning for Groundwater Sustainability Accounting for Uncertainty and Costs: an Application to California’s Central Valley, Journal of Environmental Management, Vol. 265, 110426, June 2020.

Faunt, C., ed. (2009). Groundwater Availability of the Central Valley Aquifer, California: U.S. Geological Survey Professional Paper 1766, 225p. USGS Professional Paper 1766: Groundwater Availability of the Central Valley Aquifer, California.

Hansen, J. A., Jurgens, B. C., & Fram, M. S. (2018). Quantifying anthropogenic contributions to century-scale groundwater salinity changes, San Joaquin Valley, California, USA. Science of the total environment, 642, 125-136.

Harou, J. and J. Lund (2008). Ending groundwater overdraft in hydrologic-economic systems, Hydrogeology Journal, Volume 16, Number 6, September, pp. 1039-1055.

Howitt, R., Kaplan, J., Larson, D., MacEwan, D., Medellín-Azuara, J., Horner, G., Lee, N. The Economic Impacts of Central Valley Salinity. Final Report to the State Water Resources Control Board Contract. March 2009.

Marques, G., J. Lund, and R. Howitt (2010). Modeling Conjunctive Use Operations and Farm Decisions with Two-Stage Stochastic Quadratic Programming, Journal of Water Resources Planning and Management, Vol 136, Issue 3, pp. 386-394.

Pauloo, R.A., Fogg, G.E., Guo, Z., Harter, T. (2021), Anthropogenic Basin Closure and Groundwater Salinization (ABCSAL), Journal of Hydrology, Vol. 593, 125787, February 2021.

Pauloo, R.A., Fogg, G.E. (2021), “Groundwater Salinization in California’s Tulare Lake Basin, the ABCSAL model,”, Posted on February 21, 2021

Reilly, T., K. Dennehy, W. Alley, and W. Cunningham (2008). Groundwater Availability in the United States: U.S. Geological Survey Circular 1323, 70p. USGS Circular 1323.

Singh, A (2014). Conjunctive use of water resources for sustainable irrigated agriculture, Journal of Hydrology, Volume 519, Part B, pp. 1688-1697, November 2014.

Zhu, T., G. Marques, and J. Lund (2015). Hydroeconomic Optimization of Integrated Water Management and Transfers under Stochastic Surface Water Supply, Water Resources Research, Vol 51, Issue 5, pp. 3568-3587.

About jaylund

Professor of Civil and Environmental Engineering Director, Center for Watershed Sciences University of California - Davis
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9 Responses to Managing Water and Crops with Groundwater Salinity – A growing menace

  1. parackal oommen thomas says:


  2. Joseph Rizzi says:

    Geothermal Single Hole Closed Loop can distill all the water needed nearly anywhere on earth 24/7. It takes new ideas with open minds to realize what is available, but financing projects takes trust and a willingness to try new things. Yes, Solar troughs is another way of distilling water using the sun, but it takes up more room. With Single Hole Closed Loop all wells drilled will reach the desired heat needed for Distillation only variable is distance down to desired heat (like 300 to 500 degrees Celsius)

    • parackal oommen thomas says:


  3. Craig R Bell says:

    I can smell it coming, Big Ag will want to get taxpayer money and public credit for “retiring” land that was salt (and other chemicals like selenium) tainted by agriculture practices.

  4. digipakab says:

    wow its wonderfull!

  5. Pingback: Increasing groundwater salinity changes water and crop management over long timescales | California WaterBlog

  6. Pingback: Increasing groundwater salinity changes water and crop management over long timescales - Clean Water Now

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