El Niño does not guarantee a wet California winter. But when the outlook points toward a higher risk of heavy rainfall, saturated soils, runoff, erosion, nutrient losses, and limited field access, growers can prepare before storms arrive. This article focuses on practical steps to protect fields, adjust fertility timing, and make better nutrient decisions during prolonged wet conditions.
Author: The Organic Agronomist
Agronomic review: Tim Stemwedel, Founder & CCA
Published by: California Organic Fertilizers, Inc.
Executive Summary
A wet winter can create problems long before a field is visibly flooded.
Heavy rainfall and prolonged saturation can affect:
field access,
soil oxygen,
nutrient movement,
nitrogen availability,
erosion,
runoff,
and the timing of fertilizer applications.
The best response is not to wait until the field is too wet to enter.
Growers can reduce risk by preparing drainage, protecting access points, adjusting fertilizer timing, and avoiding unnecessary nutrient applications before long periods of saturated soil.
A wet-winter fertility strategy may need to rely less on one large preplant application and more on smaller, better-timed applications when the crop can actually use the nutrients.
That does not mean automatically applying more fertilizer after every storm.
Instead, growers should evaluate:
how much rain actually fell,
how long the soil stayed saturated,
soil texture,
crop growth stage,
nutrient form,
and whether the crop is showing evidence of reduced nutrient availability.
The most useful approach is to prepare for three stages:
Before the rain: improve drainage, protect field access, and review the fertility plan.
During prolonged wet conditions: avoid unnecessary traffic, monitor saturation, and watch for signs that nutrient uptake is being restricted.
After the storm: assess conditions before deciding whether supplemental fertility is needed.
The goal is not to predict exactly what El Niño will do. It is to make the farm more resilient if the winter turns wet.
Before the First Major Storm: Fix Water Movement
The first job is simple:
Give excess water somewhere to go.
Before the rainy period begins, inspect the places where water normally slows, ponds, or backs up.
Check:
drainage ditches,
culverts,
field inlets,
tailwater systems,
low spots,
road crossings,
berms,
and known areas of poor infiltration.
Remove sediment, weeds, crop residue, or other obstructions that could restrict flow.
Pay particular attention to outlets.
A ditch may be open, but if the outlet is blocked or undersized, water can still back up into the field.
Also look at where water enters the field from surrounding roads, higher ground, neighboring parcels, or irrigation infrastructure.
The goal is not to drain the field instantly.
It is to prevent avoidable ponding and give excess water a controlled path away from crop roots and traffic areas.
Why this matters agronomically
When soil remains saturated, air-filled pore space declines.
That can reduce:
root respiration,
nutrient uptake,
microbial activity,
and normal root function.
The longer saturation persists, the greater the risk of:
oxygen stress,
denitrification,
root injury,
and delayed field access.
Drainage work done before the storm is usually much easier than trying to solve the problem after the field is already saturated.
If water has nowhere to go, every other wet-weather management decision becomes harder.
Protect Field Access Before You Need It
A field can recover from heavy rain before the equipment can get back into it.
That difference matters.
If roads, turn rows, field entrances, or loading areas become impassable, growers may lose the ability to:
apply fertilizer,
make crop-protection treatments,
repair irrigation,
scout problem areas,
or harvest on time.
Before the wettest part of the season, identify the access points that are most likely to fail.
Check:
field entrances,
low sections of farm roads,
turn rows,
canal or ditch crossings,
loading areas,
and places where equipment commonly sinks or ruts.
Where practical, stabilize those areas before storms arrive.
That may mean improving drainage, adding suitable road base, reshaping a low spot, or creating an alternate access route.
Avoid creating a compaction problem while solving an access problem
Driving on saturated soil can damage soil structure and create compaction that lasts well beyond the storm.
That can reduce:
infiltration,
root penetration,
aeration,
and future trafficability.
If the field is too wet to support equipment, forcing an application may create a second problem while trying to solve the first.
This becomes especially important when fertilizer timing is tight.
A grower who expects to make in-season nutrient corrections needs to think ahead about whether the field will actually be accessible when that application window arrives.
Wet-weather fertility planning is partly a nutrient problem and partly a logistics problem. If you cannot reach the crop, you cannot correct the program.
Rethink the Fertility Plan Before the Soil Is Saturated
A wet winter can change both nutrient availability and the timing of when fertilizer can be applied.
That means the fertility program may need to change before the rain arrives.
The biggest mistake is treating a wet winter exactly like a dry one.
If a large portion of the nitrogen program is applied well before crop demand, prolonged wet conditions can increase the risk that some of that nitrogen is:
moved below the active root zone,
lost through denitrification,
immobilized temporarily,
or simply unavailable because roots are not functioning well in saturated soil.
For organic systems, timing can be even more complicated because nutrient release depends on biological activity.
Cold, saturated soils can slow mineralization at the same time the crop is experiencing restricted root activity.
That creates a timing mismatch:
the nutrient may be in the field, but not available when the crop needs it.
The practical fix
Where the crop and production system allow it, consider shifting part of the fertility program away from one large early application and toward:
smaller applications,
later applications,
split applications,
and nutrient sources that can respond more closely to actual crop demand.
This does not mean eliminating preplant fertility.
It means avoiding a situation where too much of the season’s nitrogen is committed before anyone knows how wet the winter will become.
A more flexible fertility plan gives the grower room to respond if:
rainfall is heavier than expected,
fields stay saturated,
nutrient release is delayed,
or crop demand changes.
Build in a contingency plan
Before the rainy period starts, decide:
which applications can be delayed,
which nutrients must be applied before field access is lost,
which inputs can be applied later,
and what information will trigger a supplemental application.
That information might include:
tissue analysis,
soil nitrate,
crop color,
growth rate,
root condition,
and the amount of rainfall or saturation that occurred.
The goal is to avoid both extremes:
overapplying before the rain
and
reactively overapplying after the rain
A wet-winter fertility program should preserve flexibility. The more uncertain the weather and field access, the more valuable that flexibility becomes.
What Happens to Nitrogen in Wet Soil
Wet soil does not affect every form of nitrogen in the same way.
The biggest losses usually occur after nitrogen has been converted to nitrate.
Nitrate is highly mobile in soil water. When rainfall moves water below the active root zone, nitrate can move with it. This is leaching. UC ANR notes that nitrate is the main form of nitrogen that moves below the root zone with percolating water. UC Agriculture and Natural Resources
Saturated soil creates a second loss pathway.
When oxygen becomes limited, soil microorganisms can use nitrate in place of oxygen. In the process, nitrate is converted into gaseous forms of nitrogen that can escape to the atmosphere.
This is denitrification.
The risk increases when soils remain saturated, particularly in poorly drained or heavy soils. UC ANR
Ammonium behaves differently
Ammonium is positively charged and is held more strongly by soil particles than nitrate.
That means it is generally less vulnerable to immediate leaching.
But ammonium does not necessarily remain ammonium.
Under suitable aerated conditions, soil microbes convert ammonium to nitrate through nitrification.
Once that conversion occurs, the nitrogen becomes more vulnerable to leaching and denitrification if wet conditions return.
Organic nitrogen adds another timing problem
Organic nitrogen must generally be mineralized before much of it becomes plant available.
Soil moisture normally supports microbial activity up to an optimum point. But UC ANR notes that once soils become saturated, poor gas exchange creates anaerobic conditions and increases denitrification risk. UC Agriculture and Natural Resources
For the grower, that means wet winter conditions can create several problems at once:
nitrate may leach,
nitrate may be lost through denitrification,
mineralization may not match crop demand,
and saturated roots may have difficulty taking up nutrients that remain in the soil.
This is why simply asking “How much nitrogen did I apply?” is not enough after a wet period.
The better questions are:
What form was the nitrogen in?
How long was the soil saturated?
How much water moved through the root zone?
And how much of that nitrogen is still available where the crop can reach it?
Wet weather does not automatically mean all nitrogen is lost. But it can change both where the nitrogen is and whether the crop can use it.
Do Not Automatically Replace Nitrogen After a Storm
A heavy rain does not automatically mean the nitrogen program has failed.
Replacing nitrogen without first assessing what happened can create a second problem: overapplication.
The right response depends on several factors.
Start with rainfall and saturation
Ask:
How much rain fell?
How quickly did it fall?
How long did the soil remain saturated?
Did water actually move below the root zone?
Was there visible runoff or ponding?
A short, intense storm and several days of saturated soil do not create the same nitrogen-loss risk.
Consider soil texture
Loss risk is strongly influenced by soil type.
Coarser soils generally allow faster water movement and may have greater nitrate-leaching risk.
Heavier soils may hold water longer, which can increase the risk of denitrification under prolonged saturation.
Consider the nitrogen source
Nitrogen already present as nitrate is more vulnerable to movement and denitrification.
Ammonium is less mobile, although it can later be converted to nitrate.
Organic nitrogen may still be present but may not be releasing nutrients fast enough to match crop demand.
Consider crop stage
A young crop with a small root system may be more vulnerable to nutrient movement below the active root zone.
A larger crop with a deeper, more developed root system may still be able to access some nitrogen that moved downward but remained within rooting depth.
Check the crop before correcting the program
Where practical, use:
tissue analysis,
soil nitrate testing,
crop color,
growth rate,
root condition,
and recent irrigation and rainfall history.
The objective is to determine whether the crop is actually becoming nitrogen limited.
Replace only what the evidence supports
If the evidence points to a likely shortage, supplemental nitrogen may be justified.
But the corrective application should be based on:
current crop demand,
remaining season length,
likely residual soil nitrogen,
and the amount of nitrogen the crop can realistically use.
The answer should not automatically be:
“We had a big storm, so replace the nitrogen.”
It should be:
“What was probably lost, what is still available, and what does the crop need now?”
After heavy rain, diagnose first and fertilize second.
Keep Soil Covered Where Possible
Bare soil is especially vulnerable during a wet winter.
Heavy rainfall can break down surface structure, move sediment, carry nutrients off the field, and reduce infiltration.
Where the production system allows it, maintaining some form of surface cover can help slow water movement and protect the soil.
Useful options may include:
cover crops,
crop residue,
vegetated borders,
grassed waterways,
or other protective ground cover.
The goal is not simply to stop erosion.
Surface cover can also improve how water enters and moves through the soil.
Recent UC ANR field work in the Salinas Valley found that cover-cropped plots had substantially greater rainfall infiltration and less runoff and erosion than bare plots during winter conditions. (ucanr.edu)
That matters because runoff does more than move water.
It can also move:
sediment,
phosphorus,
organic matter,
and nutrients attached to soil particles.
Cover crops still need to fit the production system
Cover crops can be useful, but they are not automatically the right choice for every field.
Consider:
planting and termination timing,
available moisture,
field access,
residue management,
crop rotation,
and whether the cover crop could interfere with the next crop.
In intensive vegetable systems, lower-biomass cover crops may sometimes provide soil protection while creating less residue to manage before planting. UC ANR has specifically discussed this approach for El Niño preparation in bedded vegetable fields. (ucanr.edu)
The practical question is:
How much bare, exposed soil can be reduced before the wettest part of the season?
Even partial protection can help slow runoff and reduce erosion risk.
Keeping soil covered is one of the simplest ways to make rainfall less destructive before it becomes a problem.
Watch Phosphorus and Sediment Leaving the Field
Nitrogen is not the only nutrient at risk during a wet winter.
Phosphorus behaves differently.
Unlike nitrate, phosphorus is generally much less mobile through the soil profile. But it can still leave the field when runoff carries:
eroded soil,
suspended sediment,
organic matter,
or dissolved phosphorus.
That makes erosion control especially important on fields with elevated soil phosphorus or where phosphorus-containing fertilizers have been applied near the surface.
Focus on the movement of soil
If muddy water is leaving the field, nutrients can be leaving with it.
Watch for:
rills forming between beds,
sediment collecting at field edges,
muddy runoff entering ditches,
erosion around outlets,
and soil movement from sloped areas.
Those are signs that the field is losing more than water.
The practical fix
Reduce the energy of moving water before it carries soil away.
Depending on the production system, that may include:
maintaining surface cover,
slowing runoff,
protecting drainage outlets,
stabilizing vulnerable field edges,
maintaining vegetated filter areas,
and repairing erosion channels before the next storm enlarges them.
If phosphorus has accumulated near the soil surface, preventing sediment loss becomes even more important.
The objective is not simply to keep fertilizer in place.
It is to keep the soil that holds the fertilizer in place.
After a major runoff event
Do not assume that nutrient loss was uniform across the field.
Low areas may receive sediment while higher or sloped areas lose it.
Inspect:
eroded zones,
depositional zones,
field edges,
and drainage pathways
before making corrective nutrient decisions.
When wet weather moves soil, it can move phosphorus with it. Protecting the soil surface is part of protecting the fertility program.
When Fields Stay Wet: Change the Timing, Not Just the Rate
When soils remain wet, the first instinct is often to think about how much fertilizer to add.
The more important question may be when the crop can actually use it.
A saturated field can limit:
root respiration,
root growth,
nutrient uptake,
microbial activity,
and equipment access.
That means adding fertilizer during prolonged saturation may not solve the immediate problem.
Wait for the crop and soil to become responsive again
Before making a corrective application, look for signs that:
standing water has receded,
the root zone is beginning to re-aerate,
roots are functioning,
field access is possible without causing compaction,
and the crop is entering a period of active nutrient demand.
This is where smaller, well-timed applications can be more useful than one large corrective dose.
Match the source to the situation
If the crop needs nitrogen quickly after a wet period, the fertilizer source matters.
Materials that depend heavily on mineralization may not respond fast enough if soil conditions are still cool or biologically sluggish.
More immediately available nitrogen sources can sometimes fit that recovery window better, provided they are appropriate for the crop, production system, and organic program.
The goal is not to abandon slower-release fertility.
It is to recognize that a wet winter may create periods when the crop needs faster access to nutrients than the original program can provide.
Do not chase every pale leaf with fertilizer
Wet roots can make a crop look nutrient deficient even when nutrients are present.
Symptoms caused by poor root function can resemble true nutrient shortage.
Before correcting the fertility program, ask:
Is the crop actually deficient?
Are roots functioning?
Is the soil still saturated?
Is the problem nutrient supply or nutrient uptake?
Will another application be available when the crop needs it?
In a wet winter, timing can matter more than rate. The best corrective application is the one made when the crop can actually respond to it.
After the Storm: A Step-by-Step Decision Process
Once the rain has passed, the goal is to avoid two mistakes:
assuming everything is fine,
or assuming everything was lost.
Use a simple decision process.
Step 1: Assess the field before making a fertility decision
Look for:
standing water,
saturated zones,
erosion,
sediment movement,
damaged field entrances,
and areas where water remained longest.
Map the problem areas if necessary.
Not every part of the field will have experienced the same conditions.
Step 2: Determine whether the crop is recovering
Ask:
Is new growth resuming?
Are roots beginning to function normally?
Is crop color improving?
Are plants still showing waterlogging stress?
Is the canopy responding uniformly?
If the crop is still under oxygen stress, fertilizer may not be the first problem to solve.
Step 3: Review what nitrogen was already applied
Record:
source,
rate,
timing,
location,
and whether the nitrogen was primarily organic, ammonium, or nitrate at the time of the storm.
That helps estimate which portion of the program was most exposed to loss.
Step 4: Evaluate the likely loss pathway
Ask whether the greater risk was:
Leaching
More likely where substantial water moved through the root zone, especially in coarser soils.
Denitrification
More likely where soils remained saturated and oxygen-limited for an extended period.
Delayed availability
Possible where organic nitrogen has not mineralized quickly enough to match crop demand.
Restricted uptake
Possible when nutrients remain in the soil but saturated roots are not functioning well.
Step 5: Test before correcting where practical
Use the tools that fit the crop and production system:
soil nitrate testing,
tissue analysis,
visual crop assessment,
root inspection,
and irrigation and rainfall records.
The goal is to determine whether the crop is actually short of available nutrition.
Step 6: Estimate current crop demand
Do not replace fertilizer based only on what might have been lost.
Base the correction on:
crop stage,
expected remaining growth,
yield potential,
current nutrient status,
and the amount of nitrogen still likely to become available.
Step 7: Make the smallest effective correction
If supplemental fertility is justified, use a rate and timing appropriate to the crop's immediate need.
A smaller application followed by reassessment may be more useful than one large replacement application when weather remains uncertain.
Step 8: Recheck the crop
Do not assume the correction worked.
Follow up with:
crop observations,
tissue testing where appropriate,
and yield or quality measurements later in the season.
The goal after a storm is not to restore the original fertilizer plan. It is to rebuild the program around the conditions that actually exist now.
Wet-Winter Fertility Checklist: Before, During, and After Heavy Rain
Before the Rain
Inspect and clear drainage ditches, culverts, outlets, and known low spots.
Protect field entrances, roads, and other access points.
Review which fertilizer applications truly need to happen before the storm.
Avoid committing more nitrogen than necessary before prolonged wet weather.
Identify which nutrients or applications can be delayed.
Record current soil and tissue status where practical.
Know which fields are most vulnerable to leaching, ponding, erosion, or denitrification.
Keep soil covered where the production system allows it.
Identify backup application routes or methods if normal field access is lost.
During Prolonged Wet Conditions
Avoid unnecessary equipment traffic on saturated soil.
Watch for standing water and areas that remain saturated longest.
Monitor erosion, runoff, and sediment movement.
Do not assume pale or stressed plants automatically need more fertilizer.
Consider whether poor root function may be limiting nutrient uptake.
Avoid large corrective fertilizer applications while the crop is still unable to respond.
Record rainfall, ponding duration, and field conditions.
Immediately After Heavy Rain
Inspect the field before deciding on a fertilizer correction.
Identify where water ponded, infiltrated, or ran off.
Check for erosion and sediment deposition.
Review the nitrogen source, rate, and timing used before the storm.
Consider the likely loss pathway:
nitrate leaching,
denitrification,
delayed mineralization,
or restricted root uptake.
Check whether the crop has resumed active growth.
Use soil nitrate or tissue testing where appropriate.
When the Field Reopens
Avoid entering until the soil can support equipment without excessive compaction.
Reassess crop condition and nutrient demand.
Make smaller, targeted corrections rather than automatically replacing the original fertilizer rate.
Choose nutrient sources that fit the crop's immediate need and expected response time.
Split corrective applications when continued wet weather remains possible.
Recheck the crop after the correction.
Before the Next Storm
Ask:
What did this storm teach us?
Where did water accumulate?
Which access points failed?
Where did erosion occur?
Which parts of the fertility plan were too inflexible?
Which applications could have been delayed?
Did the crop actually need supplemental fertility?
What should be changed before the next rain event?
A wet-winter plan should become more precise after every storm. The objective is not simply to recover from rainfall, but to reduce the damage and uncertainty created by the next one.
Conclusion
A wet El Niño winter does not guarantee disaster, and it does not mean growers should automatically add more fertilizer.
It does mean the production system needs more flexibility.
The most useful preparation happens before the rain:
improve drainage,
protect field access,
reduce erosion risk,
and avoid locking too much of the fertility program into early applications.
Once soils become saturated, nutrient behavior changes.
Nitrate can move or be lost, organic nitrogen may not become available on schedule, and roots may struggle to take up nutrients even when they are still present in the soil.
That is why the best response is not simply:
“Add more nitrogen.”
It is:
“Figure out what changed, what is still available, and what the crop needs now.”
A wet-winter fertility program should be able to adjust as conditions change.
That may mean:
delaying part of the nitrogen program,
splitting applications,
using more responsive nutrient sources when appropriate,
waiting until roots are functioning again,
and making smaller corrections based on current crop demand.
The same principle applies to the rest of the field.
Protect soil from erosion. Keep drainage functioning. Preserve access. Avoid unnecessary traffic on saturated ground. Reassess after every major storm.
The goal is not to outguess the weather. It is to build enough flexibility into the farm and fertility program that heavy rain does not force bad decisions.
Key Takeaways
El Niño increases the reason to prepare, but it does not guarantee a wet California winter.
Clear drainage systems before the wettest part of the season.
Protect roads, field entrances, and critical access points before storms arrive.
Avoid unnecessary equipment traffic on saturated soil.
Keep soil covered where practical to reduce runoff and erosion.
Do not assume all nitrogen is lost after heavy rain.
Nitrate is more vulnerable to leaching and denitrification than ammonium.
Organic nitrogen may remain in the soil but become available too slowly to match crop demand.
Saturated roots can show nutrient-deficiency symptoms even when nutrients are present.
Preserve flexibility by splitting or delaying fertilizer applications where practical.
After a storm, diagnose first and fertilize second.
Base corrective fertility on crop demand, soil conditions, nutrient form, rainfall, and testing where appropriate.
When fields stay wet, changing timing may be more important than increasing rate.
Protecting soil from erosion also protects phosphorus and other nutrients.
Reassess the plan after every major storm and use what happened to improve the next decision.
References
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Suggested Citation
The Organic Agronomist. (2026). Preparing the Farm for a Wet El Niño Winter: What to Do Before the Rain Starts. California Organic Fertilizers, Inc. Agronomic review by Tim Stemwedel, Founder & CCA.
Permission to Use
© 2026 California Organic Fertilizers, Inc. All rights reserved. Readers may download, save, and print this publication for personal, educational, or internal business use. Brief excerpts may be quoted with attribution to The Organic Agronomist and a link to the original article. This publication may not be republished, altered, sold, distributed commercially, or presented as another party’s work without prior written permission from California Organic Fertilizers, Inc.
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