Manure Pit Management: What Dairy and Hog Operations Need to Know

A manure pit isn’t much to look at. Under the surface, it’s an active biological system, and what happens determines how much of that manure’s value survives until pump-out. For dairy and hog operations running liquid manure systems, pit management isn’t just about storage, it’s about what’s happening to the nutrients while they wait.

What’s Actually Happening Inside a Manure Pit

A manure pit, deep pit, or lagoon is a layered environment, not a uniform one. Near the surface, where some oxygen is present, aerobic bacteria are active, cycling nutrients as they break down organic material. 

Deeper in the pit, in low-oxygen conditions, anaerobic bacteria take over. Their job is different: anaerobic activity is largely responsible for breaking down the denser, solid material that settles toward the bottom, the layer that tends to cause the most handling headaches at pump-out.

This layering isn’t fixed, either. It shifts with temperature, with how much fresh material is being added, and with how often the pit gets agitated or disturbed. A pit that never gets mixed will develop a more pronounced crust layer at the surface and a heavier solids layer at the bottom, while a pit that’s agitated more regularly tends to stay more uniform, which generally means more consistent microbial activity throughout.

This isn’t a static process. The manure sitting in a pit today is chemically different from the manure that goes into it, and it keeps changing the longer it sits. That’s a good thing when biology is active and working efficiently. It’s a slower, less productive process when the pit’s microbial population doesn’t have what it needs to do that work well.

Crusting, Agitation, and Why Solids Build Up

Crust layers form on liquid manure systems for a fairly simple reason: fibrous material floats, and without regular agitation, it accumulates at the surface faster than biology can break it down. Over time that layer can thicken enough to trap gas underneath, complicate agitation, and make an accurate read on pit contents harder to get.

Agitation before pump-out is standard practice for a reason. It redistributes solids and nutrients that have settled or floated out of suspension, so what actually gets applied reflects the pit as a whole rather than whatever layer the pump happens to reach first. How much agitation a system needs depends heavily on how much biology is actively working through that solid material between fill-ups. A pit where anaerobic activity is keeping pace with incoming solids will crust and settle less aggressively than one where solids are simply accumulating faster than they can break down.

Dairy vs. Hog: Why Pit Contents Behave Differently

Hog manure management and dairy manure management deal with meaningfully different material, even though both often end up in a similar liquid storage system.

Dairy cattle are ruminants, and ruminants digest fiber thoroughly before it becomes manure. That means dairy manure entering a pit is often already partially broken down, with a more moderate nutrient load and a bedding mix (straw, sand, or manure solids) that adds its own carbon dynamics to the system. Sand bedding in particular changes pit management in a way that’s specific to dairy: sand doesn’t break down at all, and settles differently than organic bedding, which is worth factoring in separately from the biological side of pit management.

Hogs are non-ruminants, and their manure tends to carry a more concentrated, less-processed nutrient load, sometimes described as “hotter” because less of it has already been broken down by the animal’s digestive process. Confinement hog operations also typically use minimal bedding compared to dairy, which changes the carbon-to-nitrogen ratio the pit’s microbial population is working with, generally less carbon relative to nitrogen than a heavily-bedded dairy system.

Neither is better or worse, they’re just different starting points. Pit management that assumes all liquid manure behaves the same way is missing a real variable. An approach tuned for a well-bedded dairy pit won’t necessarily transfer directly to a minimally-bedded hog system, even though the underlying aerobic and anaerobic processes are identical.

Common Pit Management Challenges

A 2020 Manure Manager industry survey that surveys manure management broadly found that operations’ top challenges weren’t agronomic, they were transportation, application costs, and handling. 

Pits are where a lot of that handling frustration originates. Solid material that settles and doesn’t break down efficiently makes agitation harder, extends pump-out time, and can create inconsistent nutrient distribution when that manure finally gets applied.

Nutrient variability is the other recurring issue. Because pit contents depend on species, diet, bedding, and how long manure has been sitting, two pits on the same operation can carry different fertility value. This makes it harder to build a precise nutrient management plan without testing. It’s a common assumption that all liquid manure from a given operation is roughly interchangeable load to load. Yet, it’s rarely true once you actually test it.

Getting More From What’s Already in the Pit

Both of these challenges trace back to the same root cause: microbial activity that isn’t fully supported. PhycoTerra® is a microalgae-based soil amendment that feeds the aerobic and anaerobic bacteria already present in a pit, rather than leaving their activity to whatever ambient conditions happen to provide. That single input changes both how fast nutrients cycle and how manageable the material becomes over time.

In testing on stored hog manure, treating a pit with PhycoTerra produced an 8.8x increase in aerobic microbial activity and a 1.4x increase in anaerobic activity, measured 14 days after treatment. The aerobic increase is what drives faster nutrient cycling. The more modest anaerobic increase still reflects real activity happening in a much harder environment to influence, the low-oxygen depths of the pit where solid breakdown occurs.

What This Means at Pump-Out

That increase in microbial activity has a direct payoff at pump-out. A pit that’s been feeding its biology throughout the fill cycle arrives at application time with more of its fertility already unlocked, instead of leaving nutrients bound up in material that won’t finish breaking down until well after it’s spread. 

Whatever nutrient availability exists at the moment of pump-out is what actually reaches the field, not whatever might have broken down eventually given more time.

It also affects handling at the exact moment operations feel it most. A pit where anaerobic activity has kept pace with incoming solids agitates more easily and pumps more consistently than one where solids have been accumulating faster than they break down, which ties directly back to the top challenges livestock operations report: transportation, application costs, and handling.

A manure pit is easy to think of as a holding tank, something manure sits in until it’s time to move. It’s more accurate, and more useful, to think of it as an active system. I can work  for an operation or against it, depending on whether the biology inside it has what it needs. Two operations with identical pits, identical herds, and identical pump-out schedules can arrive at application day with very different amounts of usable fertility. They can also have very different amounts of hassle getting there based entirely on how well that biology was supported along the way.

If your pit has been running on ambient conditions alone, there’s real value sitting in it that’s easy to leave on the table. PhycoTerra’s Manure Value Initiative is currently enrolling livestock operations across North America for the 2026 season. Participants can earn back up to 70% of their product cost by helping measure results like these on their own operation. 

Learn more about the Manure Value Initiative.