How manure lagoons work, and why they stall

A manure lagoon is an earthen basin built to treat manure biologically, not just hold it. It carries extra dilution water so bacteria can break down organic solids in two stages: acid-forming bacteria first, then slower methane-forming bacteria. Lagoons stall when they are overloaded, cold, shock-loaded, or filling with fiber and sludge, and the first sign is usually odor.

What is a manure lagoon?

USDA NRCS defines a waste treatment lagoon as an embanked or excavated basin whose job is to reduce the nitrogen, phosphorus, and oxygen demand of the manure and cut odor (NRCS Practice Standard 359). The key word is treatment. A lagoon is a biological system you happen to pump from.

That is what separates it from a manure storage pond or basin. Purdue Extension puts it plainly: a treatment lagoon holds diluted manure for a long time to promote biological treatment, while an earthen storage holds undiluted manure and only treats it incidentally (Purdue ID-352).

You can see the difference in what comes out. Nebraska Extension describes storage manure as a slurry with a milkshake consistency that usually goes out by tank wagon or injection, while lagoon effluent is watery enough to irrigate (UNL Water).

What is inside a lagoon?

Think of a lagoon in layers from the bottom up. NRCS sizes an anaerobic lagoon by adding together:

1. Sludge storage. Room for the solids that will settle over the lagoon's life.
2. Minimum treatment volume. The permanent pool the bacteria live in. University of Missouri Extension says this volume supplies the dilution bacteria need and stays in the lagoon through every pump-down (Missouri EQ 387).
3. Manure storage. The manure, wash water, and bedding produced between pump-outs.
4. Weather. Normal rain minus evaporation, plus runoff.
5. Storm and freeboard. Room on top so a big storm does not overtop the berm.

Missouri Extension notes lagoons typically run 8 to 20 feet deep, and that deeper lagoons tend to produce fewer odors because they have less surface area and mix better as gas bubbles rise.

The layer that matters most is the one people forget: the minimum treatment volume. Pump below it and the bacteria lose their home. Let sludge fill it and the same thing happens slowly.

How does the biology actually work?

Oklahoma State Extension describes the process in two steps. First, one group of microbes breaks settled solids down into sludge and organic acids. Second, a different group converts those acids into methane and carbon dioxide. The methane formers grow slowly, so a lagoon needs enough detention time to keep them from washing out (Oklahoma State BAE-1736).

That two-step split explains most lagoon odor. Oklahoma State notes that hydrogen sulfide, ammonia, and other volatile compounds form during the acid stage and are later broken down into less odorous compounds. When the second stage keeps pace with the first, the lagoon smells musty, which Missouri Extension calls normal. When the acid formers get ahead, odor builds.

Mississippi State Extension adds two things a producer can watch for. A balanced anaerobic lagoon runs at a pH of about 7 to 8, and at 6.5 or lower odor problems follow. And a pink, reddish, or lavender color in warm weather comes from purple sulfur bacteria and indicates good lagoon action (Mississippi State P3723).

Why does a lagoon stall?

A lagoon does not usually fail all at once. It slides, and the slide almost always shows up as smell before anything else.

Cold. Biological activity drops in winter. Missouri Extension notes that the spring restart can produce odors, and that seasonal mixing in spring and fall can release them too. Mississippi State points out that lagoons are generally not used in the far northern U.S. because of cold. In the Midwest they work, but they are designed to take less loading per unit of volume than a southern lagoon, and they slow down every winter.

Overloading and shock loads. Missouri Extension says lagoons work best loaded at least weekly and ideally daily, and that large irregular slug loads cause odor. Oklahoma State lists extra organic loads such as spoiled milk or afterbirth as a cause of odor problems. Adding animals without adding lagoon volume does the same thing slowly.

Low pH. When the acid formers outrun the methane formers, pH drops. Missouri Extension recommends measuring pH often when odor is a problem and treating with hydrated lime or caustic soda if it falls below 6.7, while noting that odorous acids can be present even at normal pH.

Fiber and bedding. Missouri Extension says bedding and fibrous material break down very slowly, build sludge, and form surface crusts that interfere with pumping, and recommends keeping them out of the lagoon where possible. On dairy and cattle operations, that is easier said than done.

Sludge eating the treatment volume. Every year some solids settle that the bacteria cannot finish. Oklahoma State also lists running effluent below the maximum drawdown, disturbing the sludge blanket, and letting salts build up by not irrigating at least once a year as causes of lagoon trouble. For measuring and removing sludge, see lagoon sludge removal: what to know before you dredge.

How do hog lagoons and dairy lagoons differ?

The manure is different, so the problems are different.

Hog lagoons receive fine manure that breaks down relatively easily. Purdue Extension notes that swine manure does not form a crust the way cattle manure does. A properly sized hog lagoon's usual trouble is loading and odor: more pigs than the lagoon was built for, cold-weather slowdowns, and spring odor when activity picks back up. Many hog operations also run deep pits or pull-plug systems that feed or replace a lagoon.

Dairy and cattle lagoons receive fiber: undigested forage and bedding. Purdue notes that cattle manure typically forms a crust. That crust is a real trade-off. University of Minnesota Extension cites research crediting a natural crust with roughly 56 to 78% odor reduction and about 81% hydrogen sulfide reduction, but also notes that breaking up natural crusts takes extra time and energy at agitation (UMN Extension). Under the crust, fiber that settles builds sludge faster than it would in a hog lagoon. A thick crust is also a fly breeding surface; more on that in fly control that starts at the manure.

What keeps a lagoon working?

Most of this is unglamorous, and all of it comes from extension guidance rather than from us.

• Start it right. Missouri Extension recommends filling a new lagoon with water to one-third to one-half of design volume before adding manure, and starting in late spring or early summer so the bacteria are established before cold weather. Oklahoma State suggests seeding with sludge from an existing lagoon.
• Load it steadily. Daily or weekly beats a big slug every month.
• Protect the treatment volume. Do not pump below the minimum operating level, and track sludge so you know when it is encroaching.
• Keep solids out where you can. Research presented by Clemson University and USDA NRCS engineers found that liquid-solid separation ahead of a lagoon reduced sludge buildup by about the same percentage as the solids removed (Extension Foundation).
• Watch the signals. Musty smell and pink or purple color are good. A rotten-egg smell, a pH drifting under 7, or agitation taking longer every year are not.
• Respect the gas. Agitation releases hydrogen sulfide. Read manure gas dangers before anyone works the lagoon.

Where does PitCharger fit?

A lagoon is already a bacterial system. PitCharger adds bacteria to it when the existing population is not getting the job done, which in practice usually means the fiber that drives crust and bottom solids on dairy and cattle lagoons, or odor that has become an ongoing condition rather than a spring event.

Manure Digester is the flagship monthly treatment for pits and lagoons. LTC-E is built for high-fiber manure and crusting. N-Loc is for maximum odor reduction. A livestock producer in Mankato, Minnesota reported recovering approximately 200,000 gallons of usable lagoon capacity after treatment.

Lagoon dosing is not a one-line formula. A common monthly rate for cattle and dairy is about one gallon per 75 animals, and lagoon rates may be adjusted based on the manure already in the lagoon and the amount added each month. Most producers should notice a difference within the first month, with continued improvement through the second and third months, and significant results are normally measured after about six months. None of it replaces the basics above. Measure your sludge before you start and again after six months so you can see what changed. Work your numbers in the calculator or get a treatment plan.

Frequently asked questions

What is the difference between a manure lagoon and a manure pit?

A pit is a storage, usually concrete, often under a slatted barn floor, holding manure until it is pumped. A lagoon is an earthen basin designed with extra water so bacteria can treat the manure while it is stored. See what is a manure pit for the pit side.

Why does my lagoon smell worse in the spring?

Bacterial activity slows over winter while manure keeps coming in. When the lagoon warms, activity picks back up and odor often spikes. Missouri and Mississippi State Extension both describe spring start-up and seasonal mixing as common odor periods.

What color should a healthy lagoon be?

Mississippi State Extension says a pink, reddish, or lavender color in warm weather comes from purple sulfur bacteria and indicates good lagoon action. A healthy lagoon should smell musty rather than foul.

Should I break up the crust on a dairy lagoon?

It is a trade-off. A natural crust cuts odor and hydrogen sulfide, but it costs agitation time, interferes with pumping, and gives flies a place to breed. Many operations decide based on whether the crust is causing pumping and fly problems.

How often does lagoon sludge need to come out?

It depends on the lagoon and what goes in. NC State Extension notes sludge typically builds over 10 to 15 years, and dairy lagoons fill faster than hog lagoons. Survey the sludge every year once the lagoon has a few years on it. See lagoon sludge removal.