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Groundwater Monitoring at an Earthen Manure-Storage Structure

Red ball iconGroundwater Monitoring at an Earthen Manure-Storage Structure

Deborah J. Quade, Robert D. Libra, and Lynette S. Seigley



Groundwater quality has been monitored for two years in the immediate vicinity of three newly-constructed earthen manure storage (EMS) structures in Iowa. These structures are located in areas with differing surficial geologic materials: the Late Wisconsinan deposits of the Des Moines Lobe (DML), the Pre-Illinoian deposits of the Iowan Erosion Surface (IES), and the thick loess of western Iowa (WI). Three to seven shallow (<25 ft.) monitoring wells were installed around each structure. At two sites, wells were drilled through the berm structure on the downgradient side, while the third structure is ringed by a drainage tile that serves as a near-structure sampling point. Water levels are measured and water samples are collected monthly for nitrate-N, ammonium-N, fecal coliform bacteria, and chloride analysis. Samples are analzyed quarterly for total organic carbon, sulfate, phosphate, and other parameters. Liquid manure samples have been collected and analyzed from two of the three structures.

Seepage has been detected at the DML and IES sites. Indications of seepage have been similar at all affected monitoring wells and include: the decline or disappearance of nitrate-N and sulfate, likely in response to the anaerobic nature of the liquid; and an increase in concentrations of chloride and total organic carbon. Chloride concentrations in the berm well at the DML site are 50% of those measured in the liquid waste and, at the IES site, chloride concentrations in the berm well are equal to those in the liquid waste. Concentrations of nutrients, such as ammonium-N, phosphorus, and potassium, have currently not increased, indicating these species are being adsorbed and retained on manure solids or the compacted soils at the base of the structures. Fecal coliform bacteria have been sporadically detected in the berm wells, but are not consistently transported from the structures. In this article, we will discuss the livestock waste handling system, the hydrogeologic setting, and the results from monitoring the effect of a Des Moines Lobe EMS structure on groundwater quality during its first two years of operation.


The DML site is located in southern Hancock County. This facility is a family owned and operated facility. The owners of this facility operate a 4,500-hog finishing operation and farm 370 acres, primarily in a corn and soybean rotation. An earthen basin is used to store the manure from the hog operation. Very little biologic treatment of manure occurs in an earthen basin, thus preserving much of the nitrogen (N) content of the manure. Lagoons, on the other hand, are designed to anaerobically treat the ma- nure and reduce the N content. The solids along with much of the phosphate (P) and potassium (K) settle to the bottom of the lagoon, and ~70-80% of the nitrogen volatilizes to ammonia gas. Lagoons tend to be utilized by operations with a large number of hogs (>5000), and operations that have a small land base available for manure application. The operators of the DML site view the manure as a resource and apply it as a fertilizer to their available land base, thus reducing their purchase of commercial fertilizer.

The earthen basin is constructed of locally derived materials, which are primarily diamicton of the Morgan Mbr. To meet state requirements, the earthen basin is designed to limit seepage to no more than 1/16 inch/day and to hold manure for up to 240 days. The lagoon has a capacity or total storage of 250,000 cu ft. or approximately 1.6 million gallons of manure. Manure is pumped out of the earthen basin twice a year, in late spring and late fall. On average, ~900,000 to 1 million gallons is pumped each time. The pumped slurry is applied by a custom applicator who uses an “umbilical cord” injection system. With the “umbilical cord” method, manure is pumped directly from the earthen basin through a hose to a tractor unit in a field adjacent to the earthen basin. The tractor unit directly injects the manure a few inches below the surface. Manure is continually pumped as the tractor moves across the field. The operators of this facility utilize a crop consultant to do a grid soil sampling of the fields to determine the nutrient needs of the fields where the manure will be applied. The consultant prepares a grid map of the farm showing the levels of P, K, and N currently available. This grid map allows the custom applicator to modify application rates of manure to a field to place additional manure where soil nutrient levels are low or reduce manure rates where nutrient levels are high. It costs an estimated $6,500 per application ($13,000 a year) to use the “umbilical cord” injection method. It is estimated that the fertilizer value of this manure is $20,000-$21,000. Despite the high costs of custom application, the operators still save $7000-$8000 a year in fertilizer costs and utilize a much more environmentally-friendly application method.



Figure 1. Diagram of DML Site showing location of storage basin, monitoring wells, and hog buildings.



In December 1993, the Iowa Department of Natural Resources -- Geological Survey Bureau (IDNR-GSB) installed seven monitoring wells around the basin. Two wells were nested upgradient of the earthen basin, one well was installed through the downgradient berm wall, and four wells were installed in two well nests downgradient of the earthen basin (Figure 1). The wells were constructed of 1-1/2 inch PVC pipe and 5-foot, 0.01 slot-size PVC screens. The wells range in depth from seven to twenty feet. Polyethylene tubing, ” in diameter, was dedicated to each well and installed in the well by drilling an angled hole in the well casing wall. Samples are drawn from the wells using a vacuum hand pump. Several well volumes are drawn from the wells prior to collecting samples.

Since January 1994, water levels have been measured and water samples have been collected monthly at this site. Water quality analyses are performed by the University of Iowa Hygienic Laboratory. Samples are analyzed for: nitrate-N, ammonium-N, fecal coliform bacteria, and chloride. Quarterly samples are also analyzed for total organic carbon and a number of other nutrients and anions (e.g., sulfate, phosphate).


Figure 2. Schematic diagram of SW to NE drilling transect and well depths at the DML Site—Hancock County, IA.



The DML site is located in a linked-depression system associated with the Altamont Moraine II (Figure 1). This hummocky plateau region (category HP) is characterized by moderate relief, and circular to rounded, irregularly shaped “hummocks” that are defined by linked-depression systems. Drilling indicates that the stratigraphy at the DML site is similar to the Davis Transect in Humboldt County. Figure 2 is a SW to NE cross section of the DML site. This transect is representative of a part of the linked-depression system which developed within the ice; sand and gravel bodies are discontinuous across the depression axis. In this moderate relief hummocky area, the Alden Mbr. cores the hummocks, while the Morgan Mbr. facies A and B sediments flank the lower side slopes of the hummock and extend into the drainageway. Figure 3 is a detailed description from Wells 6 and 7, the stratigraphic sequence at this nest is representative of linked-depression system stratigraphy.. Wells 3 and 4 are not included in the transect but are completed in Morgan Mbr. facies A and B, again demonstrating the discontinuous nature of sand and gravel bodies associated with linked-depression systems.


Name: 41-Kanawha-7 County: Hancock
Company: D. Thompson farm
Parent Material: glacial diamicton Vegetation: picked row crop
Loc. (Q's): SE, NE, SW, NW Sec. 20 T. 94N R. 24W
Quad: Olaf Elevation: 1201 ft.
Slope: 0-1% Landscape Position: nearly level surface in drainageway
Date Drilled: 12/16/93 Date Described: 12/16/93
Descrip. By: D. Quade and E. A. Bettis III
Depth (cm) Soil Horizon (w. zone)


DeForest Formation: undiff.
0-90 Ap very dark gray (10YR3/1) silty clay loam, weak fine granular, friable, noneffervescent, abrupt boundary
90-110 AB very dark gray (10YR3/1) silty clay loam, weak very fine to fine subangular blocky, friable, noneffervescent, clear boundary
110-140 Bg1 very dark gray to greenish gray (5Y3/2-5GY5/1) silty clay loam, weak fine subangular blocky, friable, noneffervescent, clear boundary
140-180 Bg2 greenish gray (5GY5/1) silty clay loam, weak fine to medium subangular blocky, friable, noneffervescent, clear boundary
180-244 BCg


greenish gray (5GY5/1) loam diamicton, weak fine subangular blocky, friable, noneffervescent, few fine prominent strong brown (7.5YR4/6) mottles, clear boundary
Dows Formation
244-352 2Cg


Morgan Member, facies A

greenish gray to dark gray (5GY5/1-2.5Y/N4) loam diamicton with common fine pebbles (0.5 cm in diameter), massive, firm, moderate effervescence, common medium prominent strong brown (7.5YR4/6) mottles, clear boundary

352-395 2C1


dark gray (2.5Y/N4) loam diamicton with few fine pebbles (0.5 cm in diameter), massive, firm, moderate effervescence, common vertical joints with medium continuous strong brown (7.5YR4/6) coatings along faces, abrupt boundary
Dows Formation
395-594 3c


Alden Mbr.

very dark gray (2.5Y/N3) loam diamicton, few fine pebbles (<0.5 cm in diameter), massive, very firm, strong effervescence

Remarks: mapped Webster clay loam; 7.6 cm diameter core.

Kanawha-7 completed at 352 cm.

Figure 3. Stratigraphic log and description for Wells 6 and 7 at the DML Site.



Linked-depression systems link the hummocky uplands and serve as an “interconnected” drainage network to nearby streams, (i.e. the West Branch of the Iowa River at this site). A geologic map of Hancock County indicates the location of former ice margins, the extent of associated outwash (alluvial aquifers) and the locations of permitted EMS sites. Valley train deposits, outwash plains, and alluvium are mapped as alluvial aquifers. Discontinuous and continuous sand and gravel bodies associated with the Morgan Mbr. are included in the alluvial aquifer designation for several reasons: 1) the highly permeable nature of these units; 2) the occurrence in and adjacent to drainageways; and 3) their potential shallow hydrologic connection to nearby streams. Linked-depression systems may be viewed as a relatively high permeability, preferential pathway for shallow groundwater movement. However, the hydrologic role of the systems is complicated by the discontinuous nature of the sand and gravel bodies, and the presence of minor topographic “saddles” between individual depressions.


A number of monitoring studies have attempted to evaluate the effects of EMS structures on groundwater quality. Parker et al. (1994) provided a comprehensive review of the literature on the topic. Most of these studies were conducted in areas with relatively permeable, coarse-grained surficial deposits. EMS structures built in such environments have been shown to cause increased concentrations of chloride and nutrients, such as ammonium-N and nitrate-N, phosphorus, potassium, and other waste constituents in nearby (typically within about 400 feet) shallow groundwater. In a number of these studies, the concentration of waste constituents, while showing significant increases when a structure is first used, begin to decline at some point in time (Miller et al., 1985; Rowsell et al., 1985; Ritter et al., 1984: Sewell, 1978; Westerman et al., 1993). This response occurred within several months to several years, and is generally believed to result from sealing of the bottom and sides of the structures by the waste solids. Laboratory investigations suggest this sealing results from the physical plugging of the permeability and porosity of the structure’s bottom and sides; biological processes at the waste-structure interface may add to the formation of a seal (Barrington and Jutras, 1983).

Hegg et al. (1979) and Westerman et al. (1993) noted a variable pattern of contamination in near-structure wells, which they ascribed to localized leakage from parts of the structure, possibly as a result of incomplete sealing. Ciravalo et al. (1979) suggested that lagoon seals could be disrupted by either the drying of exposed soils and wastes on lagoon embankments when wastes are removed, or by gas release from microbial activity occurring below the seal. This could result in the intermittent release of fluids and waste constituents from EMS structures while the seal reformed. The investigations of Westerman et al. (1993) in particular show the range of effects that EMS structures may have on shallow groundwater quality. While some of the downgradient (“downflow”) wells they monitored showed the rising-falling concentration trend that appears to accompany sealing, other wells showed increasing concentrations during a five-year period, while yet others remained at “background” levels throughout the monitoring.

Nitrate-N is a contaminant of concern in investigations of EMS structures. Nitrate is not typically a significant constituent of liquid livestock wastes; rather, nitrogen is present as ammonium- or organic-N in this anaerobic liquid. However, seepage from EMS structures has been shown to generate relatively high concentrations of nitrate in downgradient groundwater (Westermann et al., 1993). As seepage enters the groundwater system and flows away from the structure, aerobic conditions are often encountered, resulting in the oxidation of ammonium- and organic-N to nitrate.

Miller et al. (1976) examined the accumulation of nutrients in soils beneath four earthen hog waste lagoons in Ontario. Two of these were built on relatively sandy materials, similar to those discussed above. The others were built on either clay-loam glacial till or lacustrine clays -- fine-grained materials similar to those present in Iowa. Significant accumulation of nutrients occurred to depths of over 10 feet below the lagoons built on sandy deposits. In contrast, the nutrient build-up was largely contained within one foot of the bottom of the lagoons built on fine-grained deposits.


Background samples were collected from the monitoring wells in January 1994, prior to filling the earthen basin. Concentrations of nitrate-N, chloride, and sulfate in six of the wells were relatively uniform, ranging from 15-20 mg/L N03-N, 18-35 mg/L chloride, and 24-38 mg/L sulfate. The relatively uniform concentrations of these ions, and the relatively high NO3-N concentrations, result from the long history of row-crop agriculture on the land where the basin was built. Background values from the Kan-6 well, which is the only well fully completed in the Alden Mbr., were much different than the other six wells. Nitrate-N was lower (<1 mg/L), while chloride (40 mg/L) and sulfate (94 mg/L) values were higher than concentrations from the other six wells at this site. The lack of nitrate at this well suggests denitrification occurs within the unoxidized Alden Mbr. sediments. A slurry sample from the basin itself was collected in december 1994. That sample contained 840 mg/l of chloride, <0.1 mg/L N03-N, and 2200 mg/l ammonium-N. Concentrations of these liquid-waste constituents likely change with time, for a variety of reasons (Westermann et al., 1993). However, these concentrations indicate the general strength of the contaminant source.


Figure 4. Water quality results from the #5 berm well, inverted triangles represent pump out periods.


Indications of seepage from the basin to the water table have been detected at the berm well and at one downgradient well nest (wells #6 and #7). Figure 4 shows pertinent monitoring results from the berm well. The first sign of seepage is a sharp decline in nitrate-N concentrations that occurred in late spring of 1994. Seepage from a manure-holding structure would be highly anaerobic; nitrate is unstable in anaerobic environments, being reduced to nitrous oxides and nitrogen gas. The second indication of seepage is the slow decline in sulfate concentrations during the period of monitoring. Sulfate is also unstable in anaerobic environments, and is reduced to hydrogen sulfide gas. The third indicator of seepage is the increase in chloride concentrations, from less than 30 mg/L at the beginning of the period to over 300 mg/L by the fall of 1995. Although not shown on the graph, the increase in chloride was accompanied by--and possibly preceded by--increased concentrations of total organic carbon. Concentrations of fecal coliform bacteria have shown sporadic “spikes,” but high concentrations are not sustained. Concentrations of the nutrients phosphate and ammonium-N have not shown increases, suggesting they are being retained on manure solids or the materials immediately beneath the basin or adsorbed. If ammonium-N was being transported from the basin as readily as chloride, ammonium-N concentrations at the berm well would approach 800 mg/L. Oxidation of this ammonium-N would generate a similar concentration of nitrate-N.

The berm well has also responded hydrologically to the seepage from the basin (Figure 4). Water levels have generally increased during the period of monitoring, trending towards the level of the waste liquid in the basin. This trend is interrupted when the liquid wastes are pumped out; water levels in the berm well decline in response. Concentrations of seepage constituents do not increase significantly in the periods following waste removal, as suggested by Cirvalo et. al. (1979). Rather, chloride concentrations show a tendency to decline or level off during these periods. This is likely in response to the reversal in hydraulic gradient caused by pumping out the basin.


Figure 5. Water quality results from the #7 downgradient well, inverted triangles represent pump out periods.


Indications of seepage from the basin have also been detected at the downgradient well nest of well #6 (19 feet deep) and well #7 (12 feet deep). These wells are located about 150 feet downgradient from the structure. Figure 5 illustrates that water quality trends at these wells are similar to those at the “berm” well--a decline in nitrate-N and sulfate concentrations and an increase in chloride concentrations. However, chloride concentrations at this well nest are lower than the berm well, typically by about 60%. As was the case for the berm well, transport of ammonium-N and phosphate has not occurred at wells #6 and #7, while organic carbon concentrations have increased. Fecal coliforms are rarely detected at these wells.

Trends in water quality are less clear at the other downgradient well nest (well #3, 13 ft. deep and well #4, 7 ft. deep). Chloride concentrations have remained relatively unchanged at these sites, however, nitrate-N and sulfate concentrations have shown a decreasing trend (approximately one-half of the background concentrations), while total organic carbon concentrations have increased sharply. At wells #5, #6, and #7, decreases in both nitrate-N and sulfate concentrations preceded chloride increases by several months. If decreases in nitrate-N and sulfate are precursors to chloride increases, then recent results for nitrate-N and sulfate suggest an increase in chloride concentrations may occur in the near future.

The IES site, a two-stage lagoon site, located in eastern Iowa and constructed on pedisediment and weathered Pre-Illinoian diamicton, has shown very similar trends to the DML site. Samples have been collected since October 1993 from the 5 monitoring wells installed at this site. Indications of seepage from the lagoon have been noted at the berm well and two downgradient wells. Monitoring results show that nitrate-N concentrations were low initially and have remained low; the lagoon was not built on recently row-cropped land. The main indication of seepage is the increase in chloride and organic carbon concentrations that has occurred particularly since September 1994. Sulfate concentration have shown a decline, and concentrations of phosphate, ammonium-N, and fecal coliform bacteria have remained low. Indications of seepage have not been detected at the western Iowa site. If seepage is occurring from this basin, it may be masked by the large volume of shallow groundwater discharged by the tile-drain that rings the site.


The results discussed above are from only three of the over 500 earthen manure-storage structures that have been constructed in Iowa in the last 5 years. These structures are relatively new, having been in use two years or less. Monitored sites are also "moderately-sized" structures. Therefore, this study should be considered a preliminary look at the effects of EMS structures on groundwater quality. The results indicate that seepage to the water table is occurring at the DML and IES sites. Indications of this seepage are similar at all affected monitoring wells, and include rising concentrations of chloride and organic carbon, and declining concentrations of sulfate and nitrate-N. Concentrations of phosphate and ammonium-N have not changed from background conditions. Note that if ammonium-N is not retained in a waste structure, it may be transported by groundwater away from the structure to an aerobic environment and converted to nitrate. Fecal coliform bacteria do not appear to be transported from these structures by groundwater. If numerous other structures are responding similarly, this study suggests a need to avoid citing EMS structures in environmentally sensitive areas. On the Des Moines Lobe, this would include linked-depression systems, where preferential pathways for groundwater movement to nearby wetlands, streams and alluvial aquifers may exist.

The main indicator of fluid movement from the structures, chloride, is a naturally-occurring constituent of water. When combined with sodium, it comprises table salt. There is a U.S. E.P.A. Secondary Drinking Water Standard, applicable for Public Water Supplies, established for chloride at 250 mg/L. At concentrations above this secondary standard, chloride may give drinking water a salty taste; there are no healthrelated implications for this standard. Seepage from the sites currently monitored is very unlikely to impact drinking-water supplies.

The monitoring to date suggest these structures are having a lesser impact on groundwater quality than most of those cited in the literature. This, in all probability, is the result of Iowa’s relatively fine-grained soils and their significant clay content, which allow for less seepage and which adsorb species such as ammonium-N. However, the results are viewed as preliminary, and are from less than one percent of the permitted structures in the state. Are they typical of structures in Iowa? Are similar results to be expected of other structures constructed of and on similar geologic materials? Will the character of the fluid seeping from the structures change as structures age? Finally, can these findings be extrapolated to larger EMS structures?


Funding for this project is provided, in part, by the (U.S. EPA)-Region VII-Nonpoint Source Program. We acknowledge the support of the University of Iowa Hygienic Laboratory, particularly the efforts of Nancy Hall and George Hallberg. Ubbo Agena, IDNR-Environmental Protection Division, and George Hallberg were instrumental in planning and securing funding for this work. Staff from the U.S.D.A.-Natural Resources Conservation Service surveyed and provided elevations for pertinent points at each site. Last, and far from least, we acknowledge the owners of the sites for cooperating and taking an active interest in this venture.


Barrington, S.F., and Jutras, P.J., 1983, Soil sealing by manure in various soil types: A.S.E.A. Paper #83-4571. St. Joseph MI, 17 p.

Ciravalo, T.G., Martens, D.C., Hallock, D.L., Collins, E.R. Jr., Korngay, E.T., and Thomas, H.R., 1979, Pollutant movement to shallow ground water tables from anaerobic swine waste lagoons: Journal of Environmental Quality, v. 8, #1, p. 126-130.

Hegg, R.O., King, T.G., and Wilson, T.V., 1979, The effects of groundwater from seepage of livestock manure lagoons: Clemson University WRRI Technical Report #78, Clemson, SC.

Miller, M.H., Robinson, J.B., and Gallagher, D.W., 1976, Accumulation of nutrients in soil beneath hog manure lagoons: Journal of Environmental Quality, v. 5, #3, p. 279-282.

Miller, M.H., Robinson, J.B., and Gillham, R.W., 1985, Self-sealing of earthen liquid manure storage ponds: I. A case study. Journal of Environmental Quality, v.14, #4, p. 533-538.

Ritter, W.F., Walpole, E.W., and Eastburn, R.P., 1984, Effect of an anareobic swine lagoon on groundwater quality in Sussex County, Delaware: Agricultural Wastes, Elsevier Applied Science Publishers, England, p. 267-284.

Rowsell, J.G., Miller, M.H., and Groenevelt, P.H., 1985, Self-sealing of earthen liquid manure storage ponds: II. Rate and mechanism of sealing: Journal of Environmental Quality, v. 14, #4, p. 539-543.

Parker, D.B., Schulte, D.D., Eisenhauer, D.E., and Nienber, J.A., 1994, Seepage from animal waste lagoons and storage ponds - regulatory and research review, in Proceedings, Great Plains Animal Waste Conference on Confined Animal Production and Water Quality: Balancing Animal Production and the Environment, Great Plains Agricultural Council publication #151, p 87-98.

Sewell, J.L., 1978, Dairy lagoon effects on groundwater quality: Transactions of the A.S.A.E., v. 21, p. 948-952.

Westerman, P.W., Huffman, R.L., and Seng, J.S., 1993, Swine-lagoon seepage in sandy soil: A.S.A.E. paper #93-4527, 32 p.


Adapted from: Hogs, Bogs, & Logs: Quaternary Deposits and Environmental Geology of the Des Moines Lobe: Iowa Department of Natural Resources, Geological Survey Bureau, Guidebook Series No. 18, 1996, p. 141-153