Home News Dairy Industry Flooding and Waterlogging Damage in Alfalfa – What to Do?

Flooding and Waterlogging Damage in Alfalfa – What to Do?

Sacramento, Calif., (January 20, 2017) – When are seasonal heavy rains welcomed but worrisome?   When rains fill reservoirs, but also turn fields into seas of standing water!

Such has been the case in northern California, which has seen torrential rains in recent weeks. After 5 years of intensive drought, the 2016-2017 rains are a welcome relief, but pose a danger to many crops including alfalfa.

It seems strange that we’re discussing water damage a few months after discussing (lack of) water stress!

Ah, the ups and downs of agriculture!

What are the mechanisms for flood damage? Alfalfa grown in Mediterranean and desert climates is still alive, green and growing during winter periods and thus subject to water damage during floods. This is unlike colder regions where alfalfa is very dormant and brown during winter months (but damage can occur in those areas as well).

The extent of either death or damage depends upon temperature, drainage, alfalfa growth status (young vs. old, active vs. dormant), and duration of flooding. The mechanisms for damage include:

  • Lack of Oxygen—Alfalfa roots must ‘breath’ just like humans, and respiration is reduced under waterlogging. If severe, lack of oxygen can cause death or lots of damage.
  • Temperature—Damage is greater under warm temperatures vs. cold due to increases in respiration rates (in plants and soil microorganisms). Hot temperatures can kill alfalfa within hours, but the crop can survive for days under cold temperatures.
  • Death of fine root hairs—Fine root hairs are particularly damaged during waterlogging and must be regenerated later if the plants survive. These are critical for nutrient and water uptake later.
  • Root Pruning. Saturated sub-surface layers can cause root pruning below that level (e.g. root pruning at 12” plow pans). These roots may recover but are damaged.
  • Micronutrient availability –Under reducing conditions (low oxygen), iron and other micronutrients may become unavailable for plant growth due to excess bicarbonates or other mechanisms including root damage.
  • Disease and pests—Since saturated soil conditions favor disease organisms, Phytophora, nematodes, and other organisms can gain the upper hand over a weakened alfalfa plant.
  • Weeds—Aggressive cold-favoring, flood-tolerant winter weeds can completely dominate alfalfa stands weakened by flooding.
  • Nodules— The Rhizobium nodules are weakened or damaged under flooded conditions, resulting in reduced nitrogen fixation.

How long does it take to do damage? This will depend upon variety, temperature and soil drainage characteristics. Dormant varieties under cold conditions may tolerate some submersion for several days; actively growing plants less so. Sometimes it could be months before damage is noticed.

We expect greater damage during late spring flooding vs. January flooding. Winter flooding causes less damage due to the plants slower physiological processes. Also, moving water is less harmful than standing water, containing more oxygen. Soils that rapidly drain after flooding exhibit less crop damage. Drainage limitations may affect plants many months after flooding occurred.

What to do?  After the intense flooding, when fields have drained, inspect roots and crowns for damage caused by anaerobic (without oxygen) conditions in the soil. Dig up roots and examine their health. Do you see greater disease in crowns or center of roots? Roots that are soft and compress easily when squeezed may be damaged beyond hope. If roots are beginning to release a strong odor, they likely won’t recover. If roots are white, they may Assess your stand-if the plants recover, will you have an adequate stand? Dig up roots and see if soil impediments have caused greater damage 12-16” below the surface (root pruning). Keep an eye on the plants, inspecting for damage and yield throughout the following summer; sometimes disease development is delayed with weakened plants succumbing to damage months later.

Seedling Fields. Newly-seeded fields, especially those seeded late in the previous fall, are the most susceptible to damage from saturated soil conditions. Seedling alfalfa has small weak roots which can die quickly from oxygen deprivation. Seedling plants are also much more susceptible to diseases such as Phytophora and Pythium.

Ideas for flood-damaged seedling fields:

  • Assess stand of the new seeding. If less than about 15-20 plants/ft2, or with large gaps, consider mitigation measures.
  • Overseed with alfalfa to improve the stand – if this is done early in the spring it can be successful. However, pay attention to herbicide issues (residual herbicides), and it will be more difficult to control weeds due to different stage of development.  Light tillage or no-till can be effective.
  • Wait longer to harvest—It’s important to allow the root system to fully recover and delay first harvest as long as possible to allow root development before harvest.
  • Use caution with the use of herbicides. Crop injury is greater when the plants are injured from floods.
  • Replant: consider rotating to a summer annual and replanting in the fall. In California, safflower is a possibility, corn, sorghum, sudangrass, sunflower are options. Then start over in the fall.

NOTE: water damage in poorly-developed new stands should be a STRONG message about the advantages of early fall or late summer seeding, e.g. August-September – these fields are a lot less susceptible to cold and flooding damage than November-planted seedlings.

Established Fields. Established fields can exhibit loss of stand, greater weed intrusion, and have lots of disease issues under flooding conditions. Nematodes are another problem in addition to oxygen deprivation.

Ideas for flood-damaged established fields:

  1. Assess the stand – if less than about10-12 plants/ft2 with lack of vigor or with large gaps, consider mitigation measures or replant decisions.
  2. Re-seeding of small areas in spring may be useful where alfalfa has completely died out and a new seed bed is formed.  However, reseeding of alfalfa into existing stands has had limited success – this is more successful with young vs. older stands.
  3. Use of glyphosate-resistant varieties is very helpful with overseeding alfalfa into existing alfalfa due to flexibility in weed management.
  4. Interseeding alfalfa plus red clover, berseem clover, or grasses may be better suited in problem areas where developing a new seed bed is not possible. This can be done no-till. An annual grass may enable forage production with later fall planting in rotation.  Plant early!
  5. Caution is advised on the use of herbicides when plants are stressed from floods. If weed control is necessary, use lowest label rates. Avoid the use of herbicides that are foliar systemic or absorbed through the roots.
  6. Delay first harvest until 10% bloom or longer. This will increase carbohydrate translocation to the roots and strengthen the root system.
  7. If possible, cut above the new re-growth (about four inches).
  8. Monitor and treat for weevil and aphid populations early. Stressed plants can be a preferred target and subject to increased damage by these pests.
  9. Silt deposits of over two to three inches will weaken the stand and may need to be re-graded and re-established in places.
  10. Some have suggested nitrogen (N) applications on yellowed flood damaged alfalfa.       Although this may help a little bit, generally its effects are marginal, and do not recommend N applications which are typically not economic.
  11. Hold off on irrigation until vegetative growth is substantial and allow roots time to strengthen and utilize excessive soil moisture.
  12. Manage your irrigation with quick shots of water. Any standing water beyond six to eight hours will only worsen the problem.
  13. If the alfalfa population decreases below 4-6 plants per square foot or with large gaps, the end may be near. Plan for a new crop in rotation!
  14. Land leveling: Pay attention to the leveling of existing fields. Take notes for corrections for the future, and for new plantings in low areas.
  15. On flood-prone fields, consider planting a more dormant variety.


Lack of oxygen, disease and weed intrusion are the main problems with flood-damaged alfalfa.   There are some over-seeding and inter-seeding options to consider, but allowing sufficient time for the crop to recover and treating the crop well during the recovery period is critical to allow sustained forage production after the damage has occurred.

Flooding in Yolo County Alfalfa Fields, January, 2017


Leave a Reply

Your email address will not be published. Required fields are marked *