Practical Manure Management Tips for Small Farms: Protecting Water, Soil, and Community
Seth Caines, a former student of environmental engineering and member of the Manure Lady’s poop group at UNL, has some fun with manure – and reminds us that we all can help improve the quality of the environment where we live.

Small farms play a vital role in food production, environmental stewardship, and rural communities. But small farms can also have big negative impacts on their neighbors if they are not managing their nutrients, animals, or soil in ways that protect local air and water quality. Sure, a small farm might only do a little bit of damage, but we remember what our mom told us: “Mind your manners and treat people like you'd want to be treated.” And when we apply that golden rule to farming, we see that no matter the size of the operation, we all have a role in preserving our local environment. Fortunately, with good planning and practical tools, even resource-limited farms can manage manure effectively and protect water and soil quality while reducing odor and improving fertilizer value.
Why Good Manure Management Matters
Manure is a valuable resource when it’s handled and applied correctly. But poorly managed manure can contribute to water pollution, soil nutrient imbalance, and odor concerns in nearby communities.
Water Protection Starts with Containment
Storing manure correctly is the first step toward protecting nearby waterways. When rain falls on uncovered manure piles or recently applied fields, nutrients like nitrogen and phosphorus can run off into streams or leach into groundwater. These nutrients feed algae blooms, which can damage aquatic ecosystems and degrade water quality for everyone downstream.
For small farms, manure storage options include:
- Clay-lined pits or lagoons –If you have or are considering adding a few animals to your operation you’d know that only a few animals can produce enough waste that will need designated storages. For liquid storage, a well-constructed clay liner helps prevent leaching of nutrients into groundwater and can last up to 15 years.
- Concrete or impermeable pads – For dry, stacked manure, an impermeable storage base provides a stable and easier cleanup area.
- Covered storage – Using tarps, or impermeable fabric can reduce odor and moisture infiltration for temporary manure storage.
Financial assistance is availble to help cover the cost of adding new manure storage facilities through the Environmental Quality Incentives Program (EQIP) from USDA-NRCS. Current animal feeding operations are eligible for funding that covers a wide variety of conservation practices. However, it is important to remember that approval and distribution of EQIP funds takes time, if you are considering an upgrade for your manure storages connect with your local NRCS field office and start planning at least 2 years before expecting to begin construction.
Reducing Odor with Smart Storage and Application
Odor is one of the most noticeable signs of manure mismanagement and it can create major friction with neighbors. Using covers on manure storage, composting manure, and/or timely application (when weather conditions and wind direction are favorable) all help reduce odor issues. Nebraska extension has developed a risk management and odor footprint tool to help farmers understand the potential environmental impacts of animal production or manure for their location. Check out both tools on the Nebraska Ag Site Planner.
Making the Most of Manure with Nutrient Planning
Applying the right amount of manure at the right time keeps nutrients in the soil (where crops need them) and out of waterways. Nutrient management plans help farmers match application rates to crop needs and soil conditions. Even though small animal farms and crop-only users of manure are not required to create a nutrient management plan, doing so can help to both increase the value of using manure each year and protect local waterways. A win-win situation!
Extension resources or local NRCS offices can assist with developing and implementing a nutrient management plan and get you started with:
- Soil testing
- Manure sampling
- Determining agronomic rates
- Identifying the best application windows to reduce your risk of losing nutrients due to runoff
Consider joining the manure team at one of its annual manure application training sessions to learn more about how to use manure in the best way possible.
Buffers, Vegetated Buffers and Bioretention: Natural Water Filters

When applying manure, it is important to remember that manure is never permitted to come into contact with surface water. Even if your farm doesn’t require an operating permit manure application and manure storage must be at least 30 ft from any surface water.
Even when not applying manure, if your fields slope toward a gully, stream, or pond, consider installing a vegetated buffer or bioretention area. These plant-based systems slow runoff and filter out contaminants before they reach water bodies. They're simple to build and can fit into existing farm layouts with minimal disruption.
The Bottom Line:
Every farm, no matter how big, can make a difference in protecting Nebraska’s water and soil. With a few thoughtful practices, small farms can boost crop production, improve neighbor relations, and protect their local natural resources.
This article was reviewed by Leslie Johnson and Mara Zelt