Biotrex and Soil Up said that, to recover after flooding, growers should first focus on rebuilding soil structure, organic matter, and microbial life. As damage from climate change continues to increase, one important adaptation measure is indeed to grow awareness, disseminate and adopt better practices to respond effectively in the event of extreme weather.

Valeria Verrone, founder of Soil Up, remarked to ClimateAdaptation.life what happens to soil during and post flooding: a rapid change in conditions and a parallel drastic and rapid shift in the soil biology, with particular effects on microbial community.

In a recent report, the two companies said that quick actions that help restore field operability may not support long-term soil health. They then explained the best measures.

In a nutshell, they proposed to cover crops (especially fast-establishing species), use compost and manure to stimulate microbial biomass and enzyme activity, limit tillage after flooding, maintain living roots year-round, and cover the topsoil with plant material (mulching).

Covering the crops supports root growth and, by capturing excess nutrients, stabilises the soil. 

“Root exudates feed microbes, increase microbial biomass and diversity, and support beneficial rhizosphere organisms and mycorrhizae,” explained the founder of Soil Up. 

As said, another measure comes from compost and manure, which add organic carbon and nutrients to rebuild soil fertility by stimulating microbial biomass and enzyme activity. 

The paper also argues that mulching protects the soil surface from erosion and moderates moisture and temperature, providing slow-release carbon that supports microbial activity during soil recovery. 

The experts also proposed deep-rooting plants instead of deep tillage to naturally improve the soil structure. “Root growth and microbial activity promote natural aggregation and rebuild pore networks over time”, they explained. 

After heavy rainfall or flooding, many changes in the soil remain difficult to detect. Nutrient losses, structural damage, and biological disruption may persist even when fields appear dry again. 

“Soil testing helps growers understand what actually happened in the soil and supports better recovery decisions,” explained Biotrex and Soil Up, adding that testing is most useful when it is repeated during the recovery process.

Verrone recommended testing the soil three times: immediately after the water recedes; 2-4 weeks later to evaluate early biological and chemical recovery and adjust management if needed; and during the following growing season. Possible methods include the one Biotrex is specialised in: functional indicators.

“Functional microbial indicators are particularly useful in this context. Instead of only describing which microorganisms are present, they measure what soil microbes are actually doing. For example, the Biotrex soil microbial analysis uses functional indicators such as decomposition potential, nitrogen cycling potential, and phosphorus mobilisation potential to assess microbial activity related to key soil functions,” reads the paper “Flooded Soils: What Happens Belowground and How to Restore Fields”. 

Since flooding can remove nitrogen through leaching (the extraction of a soluble substance from a solid mixture by dissolution) and denitrification (the reduction of nitrate into nitrogen gases), the technicians should immediately test for nitrogen, but not only.

“Phosphorus availability may temporarily increase due to chemical changes, while micronutrients such as iron and manganese may reach toxic levels,” said the experts. 

The paper also underlines the need to measure microbial biomass, soil respiration, enzyme activity, and metabolic activity.

“Functional indicators like decomposition, nitrogen cycling, phosphorus cycling provide insight into the recovery of key soil processes”, reads the paper.

Biotrex and Soil Up also explain that flooding and post-flood machinery traffic can damage soil structure, causing compaction and reduced aeration.

“Monitoring bulk density, aggregate stability, and infiltration rate helps determine whether soils need mechanical intervention or biological restoration.”

The paper also stresses the need to test for contaminants and pathogens, which could be introduced by floodwater.

On the other hand, they suggested that common practices could be detrimental. They listed six. 

Intensive tillage to dry the soil, which improves aeration and evaporation, allows quicker replanting, but breaks soil aggregates and microbial habitats, accelerating organic matter mineralization, and reducing fungal biomass. 

Rapid artificial drainage through pumping restores aerobic conditions and allows machinery to work again by removing excess water. On the flip side, the sudden re-oxygenation can accelerate organic matter breakdown and favour fast-growing opportunistic microorganisms.

High mineral fertilisers would compensate for the lost nitrogen, helping crops recovering quickly, but could reduce plant reliance on beneficial microbes. Additionally, it may gradually lower microbial diversity and functional efficiency.

Another common action consists in controlling for chemicals and pathogen outbreaks, but the counter-intervention through products could also disrupt beneficial soil microbes and reduce microbial functional diversity in the rhizosphere.

Farmers could also leave soil bare to speed drying, also to simplify field preparation for the next crop. At the same time, this approach increases the erosion risk and the loss of organic matter, which can then reduce microbial biomass and soil resilience.

The last set of measures has to do with the attempt to adjust pH or counteract toxic compounds that accumulate under waterlogged conditions through chemical amendments. 

“Rapid chemical shifts may stress microbial communities and favour only a limited range of microbial groups”, explained Verrone. 

At the beginning of 2026, nine destructive storms hit Spain and Portugal within a single month, causing widespread flooding and agricultural losses estimated at €750 million. 

According to the paper, human-driven climate change has increased rainfall intensity in the Iberian Peninsula by up to 36%.