Heavy rains soon after planting causing ponding will reduce plant stands due to crusting, seed decay, and diseases, see figure 1. If the water subsides in a few days, soybean stands are often still acceptable, although final yield may be impacted. Once plants have emerged the length of time soybeans survive under water depends on temperature, growth stage, cloud cover. If the plants are small and conditions are cool as well as cloudy, soybeans can survive up to a week completely submerged. Under more average summer weather they may survive for as little as 2 days. Warmer temperatures and sunlight speed up plant respiration using up available oxygen.
Flooding can be divided into two categories. 1.) Water logging when the roots are under water and 2.) complete submergence when the whole plant is under water. Water logging is more common and causes yield loss across a larger portion of the field. Yield losses may be minimal if the field is only waterlogged for a few days. If the field is waterlogged for many days, yield losses can be significant. Research has shown that water logging can reduce soybean yield over 40% during the vegetative growth stages and 50% during the reproductive stage. Yield losses are the result of reduced growth, reduced nitrogen fixation, reduced photosynthesis, and diseases. There are a number of diseases that can take advantage of the wet conditions including phytophthora, rhizoctonia, and pythium. Soil type also impacts the amount of damage. Flooded clay soils suffer more than silt loam soils when flooded (Scott et al, 1989). During the V4 growth stage, flooding resulted in a yield loss of 1.8 bu/ac per day on a clay soil and 0.8 bu/ac per day on a silt loam soil. The impact of flooding during later growing stages was considerably higher. Plant survival from submergence can be assessed within a couple of days after the water drains. Generally, by the time conditions are dry enough for a possible replant it’s clear if the plants have survived. New growth will be evident if the plants have survived.

Figure 1. Soybean flooded by excess rainfall soon after seeding.
References
1. Scott, H.D., J. DeAngulo, M.B. Daniels, L.S. Wood. 1989. Flood duration effects on soybean growth and yield. Agron J. 81:631-636.