Increasing groundwater salinity changes water and crop management over long timescales

by Yiqing “Gracie” Yao and Jay Lund

Salinity has often become a major limit for irrigated agriculture in semi-arid regions, from ancient Mesopotamia to parts of California today. A previous blog post showed that conjunctive use with more saline groundwater can differ fundamentally from freshwater aquifers. Higher salinity limits groundwater use for irrigation during dry years, when less surface water is available to dilute groundwater salinity, and increases aquifer pumping in wetter years to avoid water-logging. Brackish groundwater can no longer serves as drought storage, but becomes a supplemental water supply in all years, limited by availability of fresh surface water for diluting salts. This greatly reduces groundwater’s ability to support permanent crops and increases variability in annual crop acreage across different water years, thus reducing profit.

This post extends the analysis timescale of groundwater management with salinity to a century, examining groundwater storage management and cropping patterns as salts accumulate in an undrained aquifer. This discussion is based on results from a recent hydro-economic optimization model (Yao 2020), which conjunctively manages surface water and groundwater for irrigating a mix of annual and permanent crops over a range of dry to wet years to maximize agricultural profits. The modeling examined conditions similar to California’s western San Joaquin Valley.

The biggest change in long-term groundwater management with salinity is that more net recharge of groundwater storage and less overall pumping occurs in early decades to slow the rise in groundwater salinity. This prolongs the use of groundwater to supply some irrigation water (when diluted with available surface water), particularly for more profitable perennial crops.

With low initial groundwater salinity, greater early pumping lowers groundwater storage to a minimum allowable level, raising early profits, and groundwater recharge occurs in the last decades to recover aquifer levels (when recharge cost is most discounted). With modest groundwater salinity, costly artificial recharge occurs in early decades (Figure 1.a) when initial groundwater storage is low, to achieve the final storage target and slow accumulation of salinity to prolong the viability of more profitable perennial crops. With higher initial groundwater storage, aquifer levels are only lowered to the storage target towards the end (Figure 1.b) for the same reason.

Figure 1. Groundwater management strategy changes greatly with modest salinity (  = 500 mg/L) with a discount rate of 3.5% and final storage target of 10 MAF.

When initial groundwater salinity is high enough to reduce perennial crop yields, groundwater recharge is increased and occurs earlier to slow groundwater salination (Figure 1.a). Net extraction moves to the last decades if initial groundwater storage is high (Figure 1.b), which means profit from pumping in the first decades cannot offset losses in later decades from groundwater salinity accumulating from early pumping.

From an earlier blog post on conjunctive use without groundwater salinity, high initial planting costs and profits for perennial crops lead to maintaining perennial crop acreages as high as possible to reduce planting costs in later decades. However, in an undrained basin, as groundwater salinity grows, perennial crop acreage must shrink, driven by low fresh surface water availability in dry years to dilute more saline groundwater. However, the high value of salt-sensitive perennial crops drives the model to suppress growth in groundwater salinity in early stages to prolong crop yields.

The cost of groundwater salinity becomes huge. When groundwater salinity becomes high enough, it is no longer suitable for irrigation and must be disposed of to avoid water-logging. In our modeling, restoring the aquifer with fresher surface water never makes more profit than managing the salinated aquifer at a near-constant level and pumping away excess drainage. However, slowing the increase in groundwater salinity occurs in early decades when benefits of larger early less-impaired perennial crop acreages are less discounted. 

It is almost impossible to lower groundwater salinity without extensive artificial recharge or expensive desalination. So, over time groundwater salinity gradually increases and perennial crop acreage decreases. The loss in total profit over 10 decades from initial groundwater salinity of 500 mg/L to 1,500 mg/L can be several hundreds of million dollars. Salination diminishes groundwater’s ability to serve as a drought reservoir for drier years and eventually makes groundwater unfavorable for agricultural water supply by reducing crop yields.

Interest rates are important (Figure 2). Lower discount rates further increase the value of controlling groundwater salinity by early aquifer recovery, deferring net extraction to the last decades when the initial groundwater salinity is still low (Figure 2.a). When initial groundwater salinity is higher, more water than required is recharged to the aquifer in early decades to slow salination and prolong production, despite some recharged water being wasted to meet the final storage goal (Figure 2.b).

Figure 2. Lower discount rates cause more aggressive groundwater recharge in early decades and shift pumping to the last decades.

A drier climate worsens conditions for irrigated agriculture with groundwater salination. It is the battle between recharging the aquifer to have lower groundwater salinity for middle decades and pumping to irrigate more perennial crops to make more profit in early decades. However, a drier climate dramatically increases the cost of recharging (especially in the first decades) because less available surface water can dilute less groundwater, meaning fewer less-impaired perennial crops can be supported, while less deep percolation from crops requires more artificial recharge in wetter years for aquifer recovery, reducing annual crops. A drier climate further increases the loss from groundwater salinity, by 200 M$ in this example.

Overall, groundwater salinity changes conjunctive water management for decadal timescales, shifting pumping from drier years to wetter years, when more surface water can dilute more saline groundwater for irrigation. Groundwater salinity also changes groundwater management at longer timescales, moving artificial recharge to earlier decades and shifting pumping to later decades (only to avoid water-logging). Even with these changes, agricultural production suffers greatly from groundwater salinity, which reduces crop yields and diminishes groundwater ability to serve as a drought backup.

In undrained parts of California and the world, irrigated agriculture faces problems of excess salinity, even if groundwater overdraft ends.

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, Y. and J. Lund (2021), Managing Water and Crops with Groundwater Salinity – A growing menace,, March, 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.

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    

About jaylund

Professor of Civil and Environmental Engineering Director, Center for Watershed Sciences University of California - Davis
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