End of Season Flooding Effects on Soybeans, Harvest

Flooded soybean field in northeast Nebraska
Figure 1. Harvest is going to be challenging this year in flooded soybean fields in northeast Nebraska. (Photos by Amy Timmerman)

End of Season Flooding Effects on Soybeans, Harvest

REVISED: Oct. 13, 2023 (originally published Oct. 13, 2017)

October has gotten off to a wet start in most of the state. These rains are beneficial in helping to recharge soil moisture for the 2024 growing season. However, some areas have received several inches of rain since Oct. 1, leading to saturated soil and flooding/ponding. Considering potential impact on yield and ability to harvest these fields will be critical in the next few weeks.

Late-season flooded soybean field in northeast Nebraska
Figure 2. Late-season flooding of soybean fields in northeast Nebraska.

In general, if the soybeans were at R7 or later, the flooding will not impact the physiological yield potential. However, several other factors can impact yield when these fields are harvested, as noted in a University of Kentucky article.

  • Pod Shattering. Pre-harvest pod shatter can occur when dry pods are re-wetted. Harvest pod shatter occurs when grain moisture content is less than 13%. As the soybean moisture decreases, shatter and harvest loss increases. Remember, when assessing harvest shatter losses, approximately four soybean seeds per square foot equals one bushel per acre in loss.
  • Plant Lodging. Lodging can occur when water rapidly enters and leaves the field. Lodged plants in contact with the soil or covered with mud, silt and debris will probably result in increased deterioration of the seed and poor seed quality.
  • Sprouting in the Pod. This occurs in a two-step process. First, seeds swell to a size large enough to break open the pod. This is observed when the pods mature but frequent rains, continuous drizzle or foggy days cause water to be soaked up by the pod wall, wetting the seed. The seed then swells and breaks open the pod. Once pods are opened, more water can reach the seed. If air temperatures are above 50oF and seed moisture increases above 50%, germination will start. Aside from getting water off the field as quickly as possible, nothing can be done to prevent seeds from germinating in the pod.
  • Saprophytic Fungi. The moist, dead soybean plant material is a wonderful host for saprophytic fungi. These fungi can cause some discoloration of the soybean seeds. It is common to see clouds of black dust during harvest of affected fields. Scout your fields to assess the amount of seed damage and determine how to separate the seed.
  • Grain Quality. Check field prior to harvest. Fungal diseases such as Phomopsis seed decay and Anthracnose thrive with warm and moist conditions during soybean maturity. Increased activity can be observed if harvest is delayed. The reduction in overall seed quality can impact marketability.
  • Soybeans May Not Mature. Fields that were flooded prior to the R7 growth stage for more than 24 hours will most likely die prematurely. Expect reduced seed quality in green and off-color seed, shriveled and smaller seed.
  • Silt and Mud. When fields dry out, soil may remain on the plants. This can delay drying of the plant and cause dusty soybeans at harvest. Rain could wash some soil off the plant. Waiting to harvest “dirty” soybeans until last could keep the combine cleaner for non-flooded soybeans.
  • Submerged Soybeans. The North Carolina Soybean Association notes: "Soybeans that were submerged in floodwaters from creeks, rivers and streams are considered to be adulterated according to the Food & Drug Administration and should not enter commerce. Federal crop insurance provides that submerged soybeans be appraised at zero value. This is due to the potential for toxins in the floodwaters. Check with your insurance adjuster to confirm."

Management Considerations for Late Season Flooding

  • Scouting. Scout fields to determine the extent of flood damage and determine harvest order.
  • Harvest Order. Shattering and lodging are reasons to harvest affected fields earlier than other fields. Silt and mud are reasons for delaying harvest. Allowing fields to dry adequately can help minimize the risk of compaction. Find a balance among these factors.
  • Manage Field Areas Separately. Most fields will not be uniformly affected by flooding. Where practical, consider harvesting flooded and non-flooded field areas separately, as one harvest date may not be optimal for the whole field.
  • Crop Insurance. Heavily damaged fields may require pursuing a crop insurance claim. Contact your crop insurance provider before harvesting field(s) so a notice of loss is submitted. It is very important to clearly document any flooded areas for insurance or disaster relief assistance claims.
  • Separation. Damaged soybeans should be stored separately from other soybeans.

Storing Flood-damaged Soybeans

There is a general rule with grain storage to avoid mixing good quality and poor quality grain. This is especially true when dealing with flood-damaged soybeans where the quality had deteriorated. Sprouted, disease-damaged and discolored soybean may lower soybean grade and incur dockage at the elevator. These quality impairments will also lower storage life, often significantly.

Cleaning bins, areas around bins, and all grain handling equipment before putting grain in storage are all standard procedures to prevent contamination and extend storage life. Aeration of the grain is important to equalize temperatures throughout the grain mass. Try to avoid hot spots from forming by stirring and cooling or removing grain from the bin.

A typical soybean crop should be at 13% moisture for a six-month storage period and 12% for 12 months storage. For lower quality beans, consider drying grain to one or two points below that required for a normal crop, monitoring grain closely while in storage, and in some cases, storing this grain for only six months rather than a year.


Managing Flood Damaged Soybeans. North Carolina Soybean Association.

Flooded Soybeans Near Harvest. University of Kentucky Corn and Soybean Science Newsletter. 2006

Discolored Soybean Seed. University of Missouri Integrated Pest Management, Sept. 19, 2011.

The Bulletin. University of Illinois pest management and crop development information.

Online Master of Science in Agronomy

With a focus on industry applications and research, the online program is designed with maximum flexibility for today's working professionals.

A field of corn.