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Critical UC management tips for flood-, water logging-damaged alfalfa

Rachael Long, UC Davis. Flooded alfalfa field.
Floodwaters in a Yolo County alfalfa field in northern California in late February.
Allowing sufficient time for the alfalfa crop to recover and treating the crop well during the recovery period is critical to allow sustained forage production after flooding damage has occurred.

When are seasonal heavy rains welcome but worrisome? When rains fill reservoirs, but also turn fields into seas of standing water.

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


Alfalfa grown in Mediterranean and desert climates are 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 the winter months.

The extent of plant death or damage depends upon temperature, drainage, alfalfa growth status (young versus old, active or dormant), and the duration of flooding.

The mechanisms for damage include:

Lack of Oxygen - Alfalfa roots must breathe just like humans, and respiration is reduced under waterlogging. If severe, the lack of oxygen can cause death or heavy damage.

Temperature - Damage is greater under warm versus cold temperatures due to increased 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-inch plow pans). These roots may recover but are damaged.

Micronutrient availability - Under reduced 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, Phytophthora, 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.


This depends upon the 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 seen.


After intense flooding and 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 the crowns or the center of roots? Soft roots that compress easily when squeezed may be damaged beyond hope. If roots are beginning to release a strong odor, they likely will not recover.

If roots are white, they may affect your stand - if the plants recover, will you have an adequate stand? Dig up roots to see if soil impediments have caused greater damage 12-16 inches 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.


Newly seeded fields, especially those seeded late 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 including Phytophthora and Pythium.

Ideas for flood-damaged seedling fields include:

  • Assess the stand of the new seeding. If less than about 15-20 plants/ft2 or with large gaps then consider mitigation measures.
  • Overseed with alfalfa to improve the stand. If completed early in the spring this can be successful. However, pay attention to herbicide issues (residual herbicides). 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 herbicides with caution as crop injury is greater when plants are injured from flooding.
  • Replant: consider rotating to a summer annual and replanting in the fall. In California, safflower is a possibility. Corn, sorghum, sudangrass, and sunflower are other options. Then start over in the fall.


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

Ideas for flood-damaged established fields include:

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


The 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.

(Note: In addition to Dan Putnam, authors of this article include Umair Gull, Brenda Perez, Michelle Leinfelder-Miles, and Rachael Freeman Long.)

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