Persistent Herbicides in Compost, Manure and Hay: How to Protect Crops

You bring in a load of well-rotted horse manure or bulk compost, spread it on your beds, and a few weeks later your tomatoes look wrong. The new leaves are cupped and twisted. Some growth looks almost fern-like. There is no disease to find and no insect to blame.

A likely culprit is a small group of persistent herbicides that pass through grazing animals and survive composting. They can be used on the pasture and hay that animals eat, and they can damage sensitive garden crops at parts-per-billion levels.

This post explains how these herbicides end up in manure, compost and hay, which crops are most at risk, and how to protect your farm with good questions and a simple bioassay test you can run before you spread anything.

Key takeaways

• The main herbicides of concern are aminopyralid, clopyralid and picloram, all from the pyridine-carboxylic acid family.
• They pass through grazing animals and survive composting, so hot composting will not reliably remove them.
• They can damage sensitive crops at parts-per-billion levels. Tomatoes, peppers, potatoes, beans, peas, sunflowers and lettuce are among the most sensitive.
• Typical symptoms are cupped, twisted leaves and fern-like new growth.
• Herbicide labels restrict moving manure, hay or compost from treated forage off the farm, but materials still circulate.
• A pea or bean bioassay, growing sensitive plants in the suspect material next to a clean control, is the standard low-cost check.

What these herbicides are and why they persist

The three active ingredients most often linked to damage from contaminated inputs are:

Brand names change and products are sold under many labels, so always look for the active ingredient rather than the trade name.

What makes this group different is persistence. When animals graze treated pasture or eat treated hay, the herbicide passes through them and stays active in manure. When that manure, or bedding, hay or grass clippings containing the herbicide, goes into a compost pile, composting does not reliably break it down. The result can be a finished compost that looks, smells and tests fine for nutrients but still carries enough herbicide to harm a tomato crop.

How contamination reaches your farm

There are several routes, and most of them involve materials changing hands.

• Manure from off-farm livestock. Horse, cattle and other manures can carry residues if the animals grazed treated pasture or ate treated hay.
• Hay and straw for mulch or bedding. Hay cut from treated fields can carry residues directly to your beds, or through bedding into manure.
• Bulk compost. Composts made with manure, hay, bedding or grass clippings can concentrate residues from many sources.
• Grass clippings. Clopyralid made headlines in the early 2000s after contaminating municipal compost in Washington State, which led to state restrictions on residential lawn use.

Herbicide labels restrict moving manure, hay or compost from treated forage off the farm. But the person selling you manure or hay may not know how the field was treated, especially if the hay was bought in from somewhere else.

Which crops are most sensitive and what damage looks like

Sensitive crops

Among the most sensitive crops are:

• Tomatoes, peppers and potatoes
• Beans and peas
• Sunflowers
• Lettuce

Symptoms to watch for

• Cupped or curled leaves
• Twisted stems and leaves
• Fern-like or narrow, strappy new growth
• Damage appearing on new growth in plants grown in or near the suspect material

These symptoms can resemble other problems, so a bioassay and a conversation with your extension office are the best way to confirm what is going on.

Questions to ask before you bring material onto your farm

Use this checklist whenever you buy or accept manure, hay, straw, bedding or compost.

For manure and bedding:

• What did the animals eat, and where did their hay come from?
• Were the pastures or hay fields treated with aminopyralid, clopyralid or picloram in any product?
• Can the supplier give you that answer in writing?

For hay and straw:

• Which field was it cut from, and who managed the field?
• What herbicides were used on that field, and when?
• Ask specifically about aminopyralid, clopyralid and picloram, not just "did you spray?"

For compost:

• What feedstocks go into the compost: manure, bedding, hay, grass clippings, yard waste?
• Does the producer screen feedstocks for persistent herbicides?
• Does the producer run plant bioassays on finished batches, and can you see the results?
• Does the producer take part in the US Composting Council's Seal of Testing Assurance (STA)? STA disclosure includes a maturity bioassay along with other tests. A maturity test is useful, but ask whether it would detect herbicide damage in sensitive crops rather than assuming it does.

For organic growers:

• Does the compost meet organic process requirements under NOP Guidance 5021, or is the processed manure covered by NOP Guidance 5006?
• Have you checked the material with your certifier before applying it?

For food-safety decisions on manure-based amendments, Cornell's National GAPs Program publishes a soil amendments decision tree.

Bioassay test checklist: pea or bean test

A bioassay uses sensitive plants as the detector. It won't tell you which herbicide is present or how much, but it will tell you whether the material is likely to hurt a sensitive crop. Run it before spreading any uncertain material.

What you need

• Several small pots or trays, clearly labeled
• A representative sample of the suspect material, taken from several spots in the pile, load or bale
• A clean potting mix that you trust for the control
• Pea or bean seeds (both are among the most sensitive crops)
• A notebook or phone for dated photos

Step by step

• Collect a mixed sample. Take material from several places and depths in the pile or load and mix it well.
• Make a test mix. Fill some pots with the suspect material, or with the material mixed into clean potting mix at roughly the rate you plan to use it in the field.
• Make a control. Fill an equal number of pots with the clean potting mix only.
• Plant the same seeds at the same depth in every pot.
• Grow the pots side by side with the same light, water and temperature, so the material is the only difference.
• Watch the new growth as plants develop several sets of true leaves. Look for cupping, twisting and fern-like growth.
• Compare with the control pots. Damage in the test pots but not the controls points to a problem with the material.
• Photograph and date both sets of plants.
• Hold off spreading until the test is done and the results look clean.

Your extension office may have a detailed bioassay protocol with timing recommendations for your crops; ask them for it. If the control plants also look poor, your potting mix, watering or conditions may be the problem, so repeat the test.

If you find contamination

• Stop spreading the material and keep it separate.
• Don't sell, give away or re-compost it into other batches, which could spread the problem.
• Contact the supplier with your photos and bioassay results.
• Call your extension office to confirm the diagnosis and discuss options for affected beds and future plantings.
• Tell your certifier if you are certified organic.
• Keep records of the source, dates, test results and crop losses. If losses are significant, talk to an advisor about your options. This post is not legal advice.

What to do next

1. Treat every off-farm manure, hay and compost load as unknown until you have answers or a bioassay result.
2. Ask about active ingredients, not just trade names, and get answers in writing.
3. Run a pea or bean bioassay before spreading any uncertain material on sensitive crops.
4. Start small with new suppliers, and test on a few beds before a whole field.
5. If you sell manure or hay, keep herbicide records and share them with buyers; the label restrictions apply to you.
6. Talk to your extension office for local guidance and bioassay protocols.

Sources

• NOP 5021 Guidance on Compost and Vermicompost in Organic Crop Production (PDF) — USDA AMS (date not confirmed)
• 5006: Processed Animal Manures in Organic Crop Production — USDA AMS (date not confirmed)
• NOP 5006 Processed Animal Manures in Organic Crop Production (PDF) — USDA (December 17, 2025)
• Soil Amendments decision tree — Cornell CALS National GAPs Program (date not confirmed)