Perspectives on DairyMAR

By Thomas Harter and Helen Dahlke

Managed Aquifer Recharge (MAR) to not only store water but also to prevent unwanted flooding. In the recent executive order (N-4-23), governor Newsom provided a near-blanket permit for water managers to divert surface water from flooded streams toward groundwater recharge, an operation referred to as “managed aquifer recharge” (MAR or “FloodMAR”, Levintal et al. 2022), without the usual regulations and paperwork. The order comes on the heels of a record snowpack in California’s mountains, which is destined to melt off into roaring streams over the coming months. Californians in the Central Valley are worriedly watching the still deepening snowpack gracing their skyline. The water stored in the snowpack is well above available surface water storage that existing reservoirs provide – in some cases, reservoirs will be able to store less than a quarter of the water that is currently available as snow. 

Already, the Tulare Lake Basin is experiencing the beginning of what will likely be an extended spring flooding season that may expand into the rest of the San Joaquin Valley. Currently, flooding is building not only within but also affecting areas to the north and east of the former Tulare Lake bed, a region dotted by orchards, vineyards, and by many dairies and their manure-treated forage fields (“land application areas”). This region extends from the eastern shores of Tulare Lake to the citrus orchards along the Sierra foothills. Entire dairy herds have already been relocated and forage crops have been submerged by flood water.

Large-scale diversion of flood waters for managed aquifer recharge may provide some relief to downstream communities and agricultural lands under threat of flooding while also storing additional water in the aquifer system – saving at least some of the now historic snowpack for drier years. FloodMAR may be achieved by using dedicated ponding areas or by flooding a large number of agricultural fields, vineyards, or orchards above and beyond their irrigation needs.

FloodMAR is not for every place. Newsom’s executive order aims at maximizing the opportunities for FloodMAR. It also has some important back-stops to ensure environmental flow needs are met, that downstream water rights are not injured, and that groundwater quality is not compromised by this open invitation to landowners to capture as much water for managed aquifer recharge as they possibly can.

For administrative purposes, the back-stops needed to be simple, yet effective. The order only allows diversion of flood flows when an imminent risk of flooding is declared by a flood agency. To protect water quality, flooding of  agricultural lands can only occur on lands enrolled in their Regional Water Board’s respective nutrient management programs (e.g., Irrigated Lands Regulatory Program, Dairy Order, etc.) and only on lands that have not received fertilizer or pesticides in the last 30 days, and are not dairy land application areas (fields regularly receiving manure).

A prohibition of FloodMAR on dairy land application areas makes intuitive sense – it is a landscape potentially fraught for leaching large amounts of nitrate, and potentially other chemicals, into groundwater. Leaching risk of nitrogen (N) in the form of nitrate is a function of soil type, manure loading, and management practices (e.g. irrigation, cropping system) that control N loss to the deeper vadose zone and out of reach of  the crops’s root system. While nitrate leaching risk in heavily manured forage fields is a valid concern, even without FloodMAR (Harter et al., 2002, 2012, 2017), there actually exists little research about water quality impacts from managed aquifer recharge on manured forage fields (“DairyMAR”), in particular those that receive manure less frequently.

Dairies, flooding, and DairyMAR. The evolving potential for flooding this year, however, poses a two-fold dilemma: some dairy land application areas are, or will likely be, subjected to unmanaged (and unwanted) flooding; and the categorical prohibition of DairyMAR may take a significant fraction of land otherwise very suitable for FloodMAR out of the water management portfolio of local agencies. Two urgent questions arise out of these dilemmas: (A) What are the groundwater quality consequences of incidental flooding on dairyland application areas and (B) Are there conditions, this year or in the future, under which DairyMAR may be a reasonable and important part of the state’s and local GSAs’ MAR portfolio.

Unwanted flooding of dairy land application areas may or may not be bad for groundwater: Unmanaged and unwanted flooding of dairy farms is already occurring at some farms in the Tulare Lake Basin and may be a reality for many others later this spring, both in the Tulare Lake Basin and in the lower San Joaquin Valley, with significant potential economic consequences for the industry. But will it also cause widespread groundwater contamination due to legacy nitrate below land application areas?

Flooding of fields previously treated with manure is unlikely to cause widespread new groundwater contamination. Rather it may continue and perhaps accelerate groundwater contamination already moving through the subsurface due to historic and recent manure management. Nitrates and salts are of particular concern (VanderSchans et al., 2009; Harter et al., 2002, 2012, 2017). Under MAR conditions, the transport of legacy nitrate and salt in the vadose zone and in shallow groundwater –  whether in dairy land application areas or other irrigated lands – may be accelerated. But at the same time it may also accelerate improvement of groundwater quality, as we illustrated recently in a modeling study (Bastani and Harter, 2019). We do not anticipate risk for microbial contamination or contamination from veterinary pharmaceuticals (antibiotics specifically) is grossly enhanced under incidental flooding or under DairyMAR conditions relative to normal manure management conditions. This is due to significant natural attenuation of these contaminants in the soils and vadose zone of dairy land application areas (Watanabe et al., 2008; Watanabe et al., 2010; Li et al, 2013; Li et al, 2015). 

We lack site-specific research about the groundwater quality impact from incidental flooding of dairy land application areas or from intentional DairyMAR. But we offer some basic considerations on assessing potential impacts of unwanted or planned flooding in dairy land application areas on nitrate transport to groundwater. First, most dairy land application areas are irrigated using furrow or flood irrigation. They are therefore typically subject to significant recharge and to nitrate leaching losses even under the best of circumstances. For these irrigation conditions, two contrasting scenarios are of primary interest: incidental flooding or DairyMAR on sandy soils and incidental flooding or DairyMAR on heavier soils (loams and clays).

On sandy soils, with high infiltration rates ranging from about half a foot per day to several feet per day (under ponding), this winter’s precipitation may have already moved much of the leachable nitrate out of the root zone, where crops could otherwise take up N during the growing season (Waterhouse et al. 2020; Waterhouse et al. 2021). Nitrate leached past the root zone will be transported  through the deeper vadose zone toward the groundwater table, with or without additional flooding. Where flooding occurs, additional infiltration of nearly nitrate-free water, possibly in very large amounts, will further enhance this ongoing recharge event. On sandy soils, it is therefore conceivable that flooding – especially under managed DairyMAR conditions – may provide a benefit by significantly diluting the high nitrate recharge that may otherwise occur.

On heavier soils, possibly with significant accumulation of organic matter, flooding may lead to mineralization of some nitrate from organic nitrogen in the organic matter and it simultaneously may lead to denitrification of that nitrate due to oxygen depletion (Murphy et al. 2021). Denitrification, the microbial conversion of nitrate to nitrous gasses, is often limited in agricultural soils due to their low carbon content. But manured fields rich in organic matter could potentially facilitate more denitrification (Levintal et al. 2023). There is much uncertainty about the additional amount of nitrate – if any – that may be leached from the root zone or the deeper vadose zone due to the flooding. Because of the heavier nature of these soils, much less water leaching will occur than on sandy soils – less than one to perhaps a few inches per day during flooding. At worst, significant additional nitrate is mobilized by flooding from the organic matter pool in the soil (mostly in intermediate and heavy soils perhaps), at best, flooding/DairyMAR related recharge will create a dilution effect on this existing train of contamination in the subsurface.

There may be a possible rationale for DairyMAR in the Tulare Lake Basin. Much of the soils with highest recharge potential on the alluvial fans of the Kings, Kaweah, St. John’s, Tule, and White rivers are underneath dairy land application areas (see figure below). Hence, in the Tulare Lake Basin, significant interest may arise in DairyMAR as part of this year’s FloodMAR portfolio, specifically where and when other FloodMAR solutions have been exhausted for preventing unwanted flooding of communities and cropland, and for saving water for the next drought.

In balancing the needs for flood protection, needs for increasing groundwater storage, and the state’s mandate to protect or improve groundwater quality, there may be a place for judicious use of DairyMAR, where the following conditions can all be met:

  • away from source areas of downgradient community wells,
  • on some of the sandiest soils,
  • on land application areas with relatively lower historic land application rates, and
  • where relatively large amounts of flood water infiltration (several feet, perhaps even several tens of feet) will likely be achieved and therefore lead to significant and rapid dilution of shallow groundwater nitrate.
The California “Modified Soil Agricultural Groundwater Banking Index”, shown on the left, and the location of urban (red) and potential dairy land application areas (status: 2010: in dark brown) on the right shows that a significant fraction of the latter in the southeastern part of the Central Valley are overlying some of the soils with the highest recharge potential.

Immediate and unique monitoring opportunities exist now to assess DairyMAR. Currently lacking specific insights into groundwater quality effects of DairyMAR, this year’s accidental and planned flooding of previously manured fields provides unprecedented and important opportunities to monitor potential effects of DairyMAR practices on groundwater quality. The most critical monitoring opportunity are readily available where groundwater monitoring systems already exist and, hence, where this year’s data can be contrasted with previous years’ data to quantify risks and benefits (Central Valley Dairy Representative Monitoring Program). With additional monitoring and assessment of flooding on land application areas over the next few months and years, we would be in a better place to effectively guide future DairyMAR policies in regions where dairyland application areas make up a large part of the land suitable for moving large amounts of flood waters into groundwater storage.

Thomas Harter holds the Nora S. Gustavsson Endowed Professorship for Groundwater Resources, is a Professor of Cooperative Extension, and is chair of the Hydrologic Sciences Graduate Group. Helen Dahlke is a Professor in Integrated Hydrologic Science and leads the UCANR Water Initiative. Both work at the Department of Land, Air, and Water Resources, and are affiliates at the Center for Watershed Sciences, University of California, Davis.

Further Reading:

Bastani, M. and T. Harter, 2019. Source area management practices as remediation tool to address groundwater nitrate pollution in drinking supply wells. J.Contam.Hydrol. 226, 103521, doi:10.1016/j.jconhyd.2019.103521

FloodMAR Network:

Harter, T., H. Davis, M. C. Mathews, R. D. Meyer, 2002. Shallow groundwater quality on dairy farms with irrigated forage crops, Journal of Contaminant Hydrology 55 (3-4), pp. 287-315

Harter, T., J. R. Lund, J. Darby, G. E. Fogg, R. Howitt, K. K. Jessoe, G. S. Pettygrove, J. F. Quinn, J. H. Viers, D. B. Boyle, H. E. Canada, N. DeLaMora, K. N. Dzurella, A. Fryjoff-Hung, A. D. Hollander, K. L. Honeycutt, M. W. Jenkins, V. B. Jensen, A. M. King, G. Kourakos, D. Liptzin, E. M. Lopez, M. M. Mayzelle, A. McNally, J. Medellin-Azuara, and T. S. Rosenstock, 2012. Addressing Nitrate in California’s Drinking Water With A Focus on Tulare Lake Basin and Salinas Valley Groundwater, Report for the State Water Resources Control Board Report to the Legislature, Center for Watershed Sciences, University of California, Davis, 87p.

Harter, T., K. Dzurella, G. Kourakos, A. Hollander, A. Bell, N. Santos, Q. Hart, A.King, J. Quinn, G. Lampinen, D. Liptzin, T. Rosenstock, M. Zhang, G.S. Pettygrove, and T. Tomich, 2017. Nitrogen Fertilizer Loading to Groundwater in the Central Valley. Final Report to the Fertilizer Research Education Program, Projects 11-0301 and 15-0454, California Department of Food and Agriculture and University of California Davis, 325p.

Kolodziej, E. P., T. Harter, D. L. Sedlak, 2004. Dairy wastewater, aquaculture, and spawning fish as sources of steroid hormones in the aquatic environment, Env. Science and Technol. 38, p. 6377-6384

Levintal, E., Huang, L., García, C.P., Coyotl, A., Fidelibus, M.W., Horwath, W.R., Rodrigues, J.L.M. and Dahlke, H.E., 2023. Nitrogen fate during agricultural managed aquifer recharge: Linking plant response, hydrologic, and geochemical processes. Science of the Total Environment, 864, p.161206.

Levintal, E., Kniffin, M.L., Ganot, Y., Marwaha, N., Murphy, N.P. and Dahlke, H.E., 2022. Agricultural managed aquifer recharge (Ag-MAR)—a method for sustainable groundwater management: A review. Critical Reviews in Environmental Science and Technology, pp.1-24.

Li, X., E.R. Atwill, E. Antaki, O. Applegate, B. Bergamaschi, R.F. Bond, J. Chase, K.M. Ransom, W. Samuels, N. Watanabe, and T. Harter, 2015. Fecal indicator and pathogenic bacteria and their antibiotic resistance in alluvial groundwater of an irrigated agricultural region with dairies. J. Env. Qual. 44:1435-1447, doi: 10.2134/jeq2015.03.0139

Li, X., N. Watanabe, C. Xiao, T. Harter, B. McCowan, Y. Liu, E. R. Atwill, 2013. Antibiotic-resistant E. coli in surface water and groundwater in dairy operations in Northern California. Environ. Monit. Assess, doi:10.1007/s10661-013-3454-2

Murphy, N.P., Waterhouse, H. and Dahlke, H.E., 2021. Influence of agricultural managed aquifer recharge on nitrate transport: The role of soil texture and flooding frequency. Vadose Zone Journal, 20(5), p.e20150.

Ransom, K.M., A.M. Bell, Q.E. Barber, G. Kourakos, and T.Harter, 2018. A Bayesian approach to infer nitrogen loading rates from crop and land-use types surrounding private wells in the Central Valley, California. Hydrol. Earth Syst. Sci., 22:2739-2758, 2018, doi:10.5194/hess-22-2739-2018

Rosenstock, T. S., D. Liptzin, K. Dzurella, A. Fryjoff-Hung, A. Hollander, V. Jensen, A. King, G. Kourakos, A. McNally, G. S. Pettygrove, J. Quinn, J. H. Viers, T. P. Tomich, and T. Harter, 2014. Agriculture’s contribution to nitrate contamination of Californian groundwater (1945-2005), J. Env. Qual. 43(3):895-907, doi:10.2134/jeq2013.10.0411

Unc, A., M. J. Goss, S. Cook, X. Li, E. R. Atwill, and T. Harter, 2012. Analysis of matrix effects critical to microbial transport in organic waste-affected soils across laboratory and field scales. Water Resour. Res. 48, W00L12, 17p., doi:10.1029/2011WR010775

VanderSchans, M. L., T. Harter, A. Leijnse, M. C. Mathews, R. D. Meyer, 2009. Characterizing sources of nitrate leaching from an irrigated dairy farm in Merced County, California, J. of Contam. Hydrology 110:9-21

Watanabe, N., B. A. Bergamaschi, K. A. Loftin, M. T. Meyer, and T. Harter, 2010. Use and environmental occurrence of antibiotics in freestall dairy farms with manure forage fields, Environ. Sci. Technol., 2010, 44 (17): 6591–6600, doi:10.1021/es100834s

Watanabe, N., T. Harter, and B. A. Bergamaschi, 2008. Environmental occurrence and shallow groundwater detection of the antibiotic Monensin from dairy farms. J. Environ. Qual. 37:S-78–S-85 (2008). doi:10.2134/jeq2007.0371

Waterhouse, H., Arora, B., Spycher, N.F., Nico, P.S., Ulrich, C., Dahlke, H.E. and Horwath, W.R., 2021. Influence of agricultural managed aquifer recharge (AgMAR) and stratigraphic heterogeneities on nitrate reduction in the deep subsurface. Water Resources Research, 57(5), p.e2020WR029148. 

Waterhouse, H., Bachand, S., Mountjoy, D., Choperena, J., Bachand, P., Dahlke, H. and Horwath, W., 2020. Agricultural managed aquifer recharge—water quality factors to consider. California Agriculture, 74(3), pp.144-154.

About Andrew Rypel

Andrew L. Rypel is a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Director of the Center for Watershed Sciences.
This entry was posted in Uncategorized. Bookmark the permalink.

1 Response to Perspectives on DairyMAR

  1. Three San Joaquin EJ organizations expressed these concerns about the Governor’s executive order: Allowing landowners to flood their fields without advance analysis of impacts to groundwater quality is potentially harmful to communities surrounded by agriculture. Many of the soils in agricultural areas are poisoned by nitrates. Unpermitted groundwater recharge threatens to pull nitrates from the soil to drinking water supplies. Additionally, groundwater recharge can result in the mobilization of uranium and other heavy metals into drinking water sources.

    “We appreciate the inclusion of some safeguards, particularly the prohibition of recharge on dairy land that is highly polluted with nitrates, but these protections do not go far enough,” says Michael Claiborne, Directing Attorney of Leadership Counsel for Justice and Accountability.

    See the rest of the press release at

Leave a Reply