A manure pit is an enclosed or semi-enclosed structure used on livestock farms to collect and store animal waste, often for months at a time, before it is spread on fields as fertilizer. These pits range from shallow concrete basins to deep underground chambers built directly beneath barn floors. They are essential infrastructure on modern hog, dairy, and cattle operations, but they are also among the most dangerous spaces on any farm due to the toxic gases produced as waste breaks down.
How Manure Pits Are Designed
The most common type is a deep pit built directly under the floor of a livestock building. Animals stand on slatted floors, and their waste drops through the gaps into the pit below, where it accumulates as a thick slurry. This design keeps the barn surface relatively clean and eliminates the need for daily waste removal. The slurry sits in the pit until it is pumped out, typically once or twice a year.
Other designs include outdoor below-ground earthen pits, above-ground steel or concrete tanks, treatment lagoons, and holding ponds. Earthen pits are generally smaller and store undiluted manure. Lagoons are much larger and rely partly on biological processes to treat the waste over time, though any treatment in a simple storage pit is incidental. To prevent leaks into groundwater, lined pits use synthetic materials like high-density polyethylene sheeting. The USDA requires a minimum liner thickness of 60 mil (about 1.5 mm) for polyethylene liners holding wastewater, and pit floors must slope at least 2 percent to allow liquids and gases to drain properly.
What Happens Inside the Pit
Once manure enters the pit, microorganisms begin breaking it down in an oxygen-free environment through a process called anaerobic decomposition. Different communities of bacteria handle different stages: some break complex organic matter into simpler compounds, while others convert those compounds into gases. The major gases produced are methane, hydrogen sulfide, ammonia, and carbon dioxide.
In open or uncovered lagoons, sunlight allows photosynthesizing bacteria to develop on the surface. These organisms help reduce sulfur and nitrogen compounds, which cuts down on odor. In sealed or below-floor pits, no such process occurs, so gases build up in the headspace between the manure surface and the floor above. This is what makes below-barn pits so dangerous compared to open-air storage.
Why Manure Pits Are So Dangerous
Hydrogen sulfide is the primary killer. It is heavier than air, colorless at low concentrations, and smells like rotten eggs, but at higher levels it paralyzes the sense of smell, leaving victims unaware of the exposure. The National Institute for Occupational Safety and Health classifies 100 parts per million (ppm) as immediately dangerous to life or health. During routine pit agitation, concentrations in barn air have been measured at 131 ppm, and in the pit headspace itself, levels can spike above 421 ppm. When pit ventilation fans are turned off or inadequate, some studies have recorded concentrations exceeding 1,000 ppm in barn air. At those levels, a single breath can cause unconsciousness.
Methane, which can make up 30 to 70 percent of the gas mixture in a pit, poses a different threat: it is highly flammable and can cause explosions if an ignition source is present. Carbon dioxide and ammonia round out the toxic mix, displacing oxygen and irritating the lungs.
A review of manure-related fatalities in Iowa between 1995 and 2003 found nine deaths in seven separate incidents, accounting for roughly 1 percent of all occupational fatalities in the state. Five of those deaths involved workers at hog manure storage facilities. A broader national review covering 1975 to 2004 documented 77 fatalities linked to livestock manure storage. One of the most troubling patterns: 22 percent of those deaths were rescuers. Coworkers or family members who rushed in to help a collapsed victim were overcome by the same gases. Ten percent of fatalities in the Iowa data involved failed rescue attempts.
Agitation: The Most Dangerous Moment
Manure pits are most hazardous during agitation, the process of mechanically stirring settled solids before pumping the pit out. Solids sink to the bottom over months of storage and form a dense layer that must be broken up so the slurry can flow through pumps. When that crust is disturbed, it releases a sudden, massive burst of trapped gases into the air above.
The University of Minnesota Extension recommends a four-step protocol before any agitation begins: evacuate all people and animals from the barn, extinguish every possible ignition source including pilot lights on heaters, post warning signs at every entrance, and maximize ventilation. Workers should lower the manure level at least two feet below the barn’s floor slats before starting agitation, which helps ventilation fans move fresh air through the animal zone. Wind conditions matter too. During outdoor pumping, wind inversions can trap gases near ground level, creating invisible pockets of lethal air.
OSHA requires anyone working in or near a manure pit to wear a portable multi-gas detector that continuously monitors for hydrogen sulfide, methane, ammonia, and oxygen levels. If a worker collapses inside a pit, rescuers must never enter without a self-contained breathing apparatus or supplied-air system. The instinct to rush in has killed dozens of people over the decades.
Nutrient Value of Stored Manure
The whole point of storing manure rather than disposing of it is its value as fertilizer. Manure contains nitrogen, phosphorus, and potassium, the same nutrients found in commercial fertilizers. However, storage method matters significantly for how much nutrient value is retained. Research comparing different storage approaches found that composted manure lost only about 8 percent of its initial nitrogen, while simple stockpiling and turning lost 45 to 46 percent. Crops planted in soil treated with composted manure recovered 44 percent of the applied nitrogen, compared to just 13 to 15 percent from other storage methods.
Pit storage of liquid slurry falls somewhere in between. Because the manure stays submerged and oxygen exposure is limited, nitrogen losses are lower than in open-air piles, though some ammonia still volatilizes from the surface. The balance between retaining nutrients and managing the safety risks of enclosed storage is a central tension in modern livestock farming.
Methane Emissions and Capture
Uncovered manure pits and lagoons are a significant source of agricultural methane, a potent greenhouse gas. The EPA identifies several strategies for reducing these emissions. Anaerobic digesters are the most effective: they capture the methane produced during decomposition and either flare it or use it to generate electricity. Common designs include covered lagoons, plug-flow digesters, and complete-mix digesters. These systems can reduce methane emissions by roughly 50 percent or more compared to an uncovered lagoon.
Semi-permeable covers made from geotextile fabric, straw, wood chips, or natural crusts offer a simpler alternative. These covers reduce methane, ammonia, and odor release, though they are less effective than a full digester system. For smaller operations where a digester is not economically feasible, covers represent a meaningful step toward reducing the environmental footprint of manure storage.