Evaluation of Potential Ammonia Reductions from Covering 

Manure Storage Ponds & Manure Storage Piles in the San Joaquin Valley

As previously demonstrated in Chapter 2 of the San Joaquin Valley Air Pollution Control 

District 2015 PM2.5 Plan1, reducing ammonia (NH3) is not an effective strategy to 

reduce PM2.5 concentrations in the San Joaquin Valley because of the abundance of 

ammonia in comparison to other precursors that react with ammonia to form fine 

particulate. However, the District has adopted stringent regulations that have 

significantly reduced ammonia emissions in the San Joaquin Valley as explained in 

Appendix C of the San Joaquin Valley Air Pollution Control District 2015 PM2.5 Plan.

1

 

In addition to these stringent regulations, the following analyses evaluates the potential 

for further ammonia reductions that could result from requiring Confined Animal 

Facilities cover stored liquid manure systems and stored solid manure piles. The 

District has evaluated these options and found that there is no decisive evidence that 

covering manure storage ponds or solid manure piles will result in meaningful 

reductions in ammonia emissions from Confined Animal Facilities in the San Joaquin 

Valley.

Evaluation of Covers to Reduce Ammonia from Stored Liquid Manure

Manure storage covers have not been conclusively demonstrated to reduce total 

ammonia emissions from Confined Animal Facilities. One study performed to evaluate 

the effectiveness of porous covers for control of emissions from hog manure storage 

lagoons in Missouri found “no statistically significant reduction of ammonia emissions” 

from any of the lagoon covers because of consistently low emission rates of ammonia.

2

The consistently low ammonia emissions observed in the study may be the result of the 

high solubility of ammonia in water. 

Installing impermeable plastic covers over storage liquid manure systems 

(lagoons/ponds) would effectively convert these manure storage ponds into covered 

lagoon anaerobic digesters due to the San Joaquin Valley’s warm climate. A number of 

experts and researchers have stated that anaerobic digestion of manure actually 

increases ammonia emissions3. Covering a manure storage lagoon or pond with an 

impermeable cover will result in greater reductions of the organic matter in the 

manure. Organic carbon will be converted to methane and organic nitrogen will be 

converted to ammonia nitrogen. This leads to greater concentrations of ammonia in the 

 

1 San Joaquin Valley Unified Air Pollution Control District. 2015 Plan for the 1997 PM2.5 Standard (2015), 

http://www.valleyair.org/Air_Quality_Plans/PM25Plans2015.htm

2 Regmi, S., Ongwandee, M., Morrison, G., Fitch, M., & Surampalli, R. (2007). Effectiveness of porous 

covers for control of ammonia, reduced sulfur compounds, total hydrocarbons, selected volatile organic 

compounds, and odor from hog manure storage lagoons. Journal of the Air & Waste Management 

Association 2007 June 57(6): Pages 761-768. http://www.tandfonline.com/doi/pdf/10.3155/1047-

3289.57.6.761

3 Simpkins, D. - Michigan Biomass Energy Program (2005). Anaerobic Digester FAQs.

https://www.michigan.gov/documents/anaerobic_digester_FAQs_2005_137431_7.pdf (September 2005). 

Accessed on May 26, 2015
liquid manure. The cover prevents the ammonia from being released directly from the 

covered areas of the pond, but the greater concentration of ammonia in the lagoon 

increases the amount of ammonia released from uncovered areas and from the effluent. 

The digested manure will also have a higher pH, which will result in a greater fraction of

the ammonia nitrogen in the form of volatile NH3 rather NH4

+

that remains in the liquid 

manure. 

There have also been studies that support that anaerobic digestion of manure increases 

ammonia emissions. One study compared ammonia volatilization from undigested and 

digested manure from a dairy in Washington found that anaerobic digestion of dairy 

significantly increased the ammonia volatilization potential from liquid dairy manure.

4

Factors that contributed to increased volatilization of ammonia from the digested 

manure include: increased concentration of ammonia nitrogen, higher pH, and a greater 

fraction of the ammonia nitrogen as NH3 because of the higher pH and ionic strength of 

digested manure. Another study presented at the 2013 eXtension Waste to Worth 

Conference indicated that anaerobically digested manure may result in greater nitrogen 

loss in the form of ammonia than raw manure.5 Some simulations using process-based 

models have also indicated that installation of anaerobic digesters at Confined Animal 

Facilities can increase ammonia emissions. The United States Department of 

Agriculture (USDA) Agricultural Research Service (ARS) Dairy Gas Emissions Model 

(GEM) Reference Manual indicates that the digestion process affects the nitrogen 

fractions in the manure, a greater portion of the organic nitrogen in the raw manure is 

converted to total ammoniacal nitrogen (TAN), and that “this increase in TAN potentially 

increases the ammonia emissions from the storage and field applied effluent.”

6

 This is 

shown in a presentation in which the USDA Dairy GEM model indicated that installation 

of an anaerobic digester at a dairy farm in New York would increase total ammonia 

emissions.7

A 2013 report to the California Energy Commission (CEC) on the performance of six 

dairy digesters operating in California found that the digesters increased the amount of 

 

4 Koirala, K., Ndegwa, P. M., Joo, H. S., Frear, C., Stockle, C.O., & Harrison, J. H. (2013). Impact of 

Anaerobic Digestion of Liquid Dairy Manure on Ammonia Volatilization Process. Transactions of the 

ASABE. 56(5): Pages 1959-1966. doi: 10.13031/trans.56.10230. (See: 

http://elibrary.asabe.org/azdez.asp?JID=3&AID=44099&CID=t2013&v=56&i=5&T=1&redirType=toc_journ

als.asp&conf=t and http://bsyse.wsu.edu/wp-content/uploads/2014/06/Article-57.pdf)

5 Sun, F., Harrison, J., Ndegwa, P., Joo, H. S., Whitefield, L., & Johnson, K. (2013). Ammonia Emissions 

from Eight Types of Dairy Manure During Storage. Waste to Worth: Spreading Science and Solutions. 

Denver, CO. April 1-5, 2013. http://www.extension.org/pages/67705/ammonia-emissions-from-eighttypes-of-dairy-manure-during-storage (November 14, 2013). Accessed on May 22, 2015

6 Rotz, C.A., Chianese, D.S., Montes, F., Hafner, S., October 2014. Dairy Gas Emissions Model 

Reference Manual Version 3.1. United States Department of Agriculture (USDA) Agricultural Research 

Service (ARS) Pasture Systems and Watershed Management Research Unit. 

http://www.ars.usda.gov/Main/docs.htm?docid=21345

7 Rotz, C.A. – USDA Agricultural Research Service (2011). DairyGEM: A Software Tool for Assessing 

Emissions and Mitigation Strategies for Dairy Production Systems. Western States Dairy Producers Trade 

Association 2011 Western Dairy Air Quality Symposium. Sacramento, CA. April 20-21, 2011.

http://www.westerndairies.org/2011symposium/13Rotz.pdf, Slide 35
nitrogen in the manure converted to ammonia nitrogen.8 The document determined this

was a positive impact because it reduces the risk of nitrogen impacting water quality but

the document did not discuss the potential for higher ammonia emissions (possibly 

because this has traditionally also been considered beneficial to water quality near 

farms). A Michigan Biomass Energy Program Anaerobic Digester FAQs document 

specifically states that anaerobic digestion produces ammonia.9 Like the CEC 

document, this document mentions the benefits of reduced leaching of nitrogen to water 

but does not discuss the potential for higher ammonia emissions. The Penn State 

Extension document “The Fate of Nutrients and Pathogens During Anaerobic Digestion 

of Dairy Manure (G-71)” specifically states that “Ammonium is not destroyed during the 

digestion process, but rather, organic N is converted to ammonium during protein 

degradation. Hence, the ammonium level in the digester effluent is typically higher than 

raw manure.” and “When digester effluent is field applied, much of the ammonium will 

be released as a gas (ammonia) unless it is incorporated into the soil.”

10 It is often not 

practical to incorporate dilute liquid manure into the soil. In addition, the stringent 

regulations to protect water quality in the San Joaquin Valley limit the times that manure 

can be applied and limit when manure can be incorporated into the soil. 

It must be emphasized that covering ponds and lagoons will not reduce the amount of 

nitrogen in the manure but will increase the fraction of nitrogen that is in the form of 

volatile ammonia. The cover may suppress ammonia from manure storage but this 

ammonia is likely to be released when the manure exits the digester. If a flare or other 

combustion device is used to dispose of the gas from the covered lagoon some of the 

ammonia may even be converted to NOX during combustion. Any increases in NOX are

detrimental to the plans for attainment of air quality standards for ozone and fine 

particulate matter in the San Joaquin Valley. 

As explained above, at this time there is no definitive evidence that that covering liquid 

manure storage ponds and lagoons will decrease ammonia emissions from Confined 

Animal Facilities in the San Joaquin Valley; however, there is evidence that covering 

liquid manure storage ponds and lagoons may increase overall ammonia emissions in 

the San Joaquin Valley. Therefore, requiring Confined Animal Facilities in the San 

Joaquin Valley to incur costs to cover manure storage ponds and lagoons as a means 

to reduce ammonia emissions is not reasonable and may even be counterproductive.

 

8 Summers Consulting, LLC (2013) Energy and Environmental Performance of Six Dairy Digester 

Systems in California – Volume 1. Final Project Report Prepared for the California Energy Commission 

Energy Research and Development Division. March 2013, CEC-500-2014-001-V1. 

http://www.energy.ca.gov/2014publications/CEC-500-2014-001/CEC-500-2014-001-V1.pdf

9 Simpkins, D. - Michigan Biomass Energy Program (2005). Anaerobic Digester FAQs.

https://www.michigan.gov/documents/anaerobic_digester_FAQs_2005_137431_7.pdf (September 2005). 

Accessed on May 26, 2015

10 Penn State Extension (2006). The Fate of Nutrients and Pathogens During Anaerobic Digestion of 

Dairy Manure (G-71). http://extension.psu.edu/natural-resources/energy/waste-toenergy/resources/biogas/projects/g-71 (July 2006). Accessed on May 26, 2015
Evaluation of Covers to Reduce Ammonia from Solid Manure Storage Piles

Generally two types of solid manure are stored at dairies in the San Joaquin Valley: 1) 

separated solids, which are solids that have been removed from a liquid manure stream 

by a separation system, and 2) manure scrapings from corrals and exercise 

pens. Studies have generally shown the VOC and ammonia emissions from separated 

solids to be very low or negligible because the majority of the VOCs emitted from cow 

manure, such as alcohols and Volatile Fatty Acids, and ammonia are highly soluble in 

water and will remain in liquid when the solids are removed. Studies have also shown 

that emissions from other types of stored dairy manure (i.e. corral scrapings) are also 

very low. 

One study performed at a San Joaquin Valley dairy for the California Air Resources 

Board (ARB) to characterize emissions from different processes at California dairies 

found that ammonia emissions from separated solids piles were below the detection 

limit.

11

The District’s current dairy ammonia emission factors for separated solid piles and other 

types of stored solid manure from milk cows are as follows:

 Separated solids piles: 0.38 lb-NH3/(milk cow-yr) - 0.53% of total dairy emissions

 Solid manure storage piles: 0.95 lb-NH3/(milk cow-yr) – 1.3% of total dairy 

emissions

Given the very low ammonia emissions from solid manure storage piles, it would be 

difficult to justify costs of covers or other controls to reduce ammonia emissions from 

solid manure storage piles. There are also major safety concerns related to covering 

manure piles that are not completely dry because heat generated by biological activity 

in the manure piles will be trapped by the covers and this will increase the chances that 

the manure piles may spontaneously combust. This safety concern is not an issue once 

the piles have dried and biological activity has lessened; however, during this period, 

due the low moisture content of the manure and decreased biological activity, ammonia 

emissions are likely to be low. There are also practical concerns related to the costs of 

the materials and labor required for large manure storage piles.

Because of the extremely low ammonia emissions from solid manure, concerns about 

combustion of manure piles that are not dry, and additional costs for covering manure 

with negligible benefits in terms of ammonia reductions, requiring Confined Animal 

Facilities in the San Joaquin Valley to incur costs to cover manure storage piles to 

reduce ammonia emissions is not reasonable. However, it should be noted that District 

Rule 4570 does contain mitigation measure options for Confined Animal Facilities that 

store solid manure onsite to cover dry solid manure or separated solids with a 

weatherproof covering from October through May. In addition, Rule 4570 contains 

several measures that promote the drying of manure even prior to storage. As stated 

 

11 Schmidt, C. & Card, T. (2006) Dairy Air Emissions Report: Summary of Dairy Emission Estimation 

Procedures. May 2006. Final Report to California Air Resource Board (ARB) 

http://www.arb.ca.gov/ag/caf/SchmidtDairyEmissions2005.pdf, Page 15, Table 5.1
earlier, drying of manure decreases biological activity and thus reduces or eliminates 

the formation of both ammonia and VOC emissions. Examples of Rule measures 

included in Rule 4570 are as follows:

 Freestall Barns (Dairy CAF):

o For a large dairy CAF, remove manure that is not dry from individual 

cow freestall beds or rake, harrow, scrape, or grade freestall bedding 

at least once every seven (7) days.

o For a medium dairy CAF, remove manure that is not dry from individual 

cow freestall beds or rake, harrow, scrape, or grade freestall bedding 

at least once every fourteen (14) days.

 Freestalls (Other Cattle):

o Remove manure that is not dry from individual cow freestall beds or 

rake, harrow, scrape, or grade bedding in freestalls at least once every 

seven (7) days.

 Solid Manure/Separated Solids (Dairy CAF, Other Cattle):

o Within seventy-two (72) hours of removal from housing, either:

 Remove dry manure from the facility; or

 Cover dry manure outside the housing with a weatherproof 

covering from October through May, except for times when wind 

events remove the covering, not to exceed twenty-four (24) 

hours per event.

o Within seventy-two (72) hours of removal from the drying process, 

either:

 Remove separated solids from the facility; or

 Cover separated solids outside the housing with a weatherproof 

covering from October through May, except for times when wind 

events remove the covering, not to exceed twenty-four (24) 

hours per event.

 Solid Manure/Separated Solids (Layer & Broiler, Duck, or Turkey):

o Within seventy-two (72) hours of removal from housing, either:

 Remove all litter/manure from the facility; or

 Cover litter/manure outside the housing with a weatherproof 

covering from October through May, except for times when wind 

events remove the covering, not to exceed twenty-four (24) 

hours per event.

 Solid Manure/Separated Solids (Beef Feedlot): 

o Within 72 hours of removal from animal housing, either remove dry 

manure from the facility or, during the months of October through May, 

cover dry manure pile with a weatherproof covering, except for times, 

not to exceed twenty-four (24) hours per event, when wind events 

remove the covering; or

o Manage moisture content of manure to less than 50%.

 Land Application (Dairy CAF, Beef Feedlot, & Other Cattle):

o If the CAF applies solid manure, choose one of the following:
 Incorporate all solid manure within seventy-two (72) hours of 

land application

 Only apply solid manure that has been treated with an 

anaerobic treatment lagoon, aerobic lagoon, or digester system

 Apply no solid manure with a moisture content of more than 

50%

Rule 4550, Conservation Management Practices, also contains several measures to 

promote the drying of manure as follows:

 CMPs for Dairies

o Corral/Manure Handling; must select one of the following:

 Fibrous layer in dusty areas

 Freestall housing 

 Frequent scraping and/or manure removal

 Pull type manure harvesting equipment

 Scraping/harrowing (in morning hours)

 Shaded areas in open corrals

 Sprinkling of open corral

 CMPs for Feedlots

o Pens/Manure Handling; must select one of the following:

 Fibrous layer in working areas

 Frequent scraping and/or manure removal

 Shaded for animals

 Sprinkling

 Pull type manure harvesting equipment

 CMPs for Poultry

o Manure Handling and Storage; must select one of the following:

 Cleanout frequency

 Outdoor storage

 Time of manure spreading