Wet Soils Influence Soil Fertility

Prepared by John Heard, MAFRD Crop Nutrition Specialist (FPE)

Heavy rainfall in much of Manitoba has farmers justifiably concerned about soil fertility. Rainfall in May and early June has been 6-12 inches across southern Manitoba. The question is what impact this has on nutrient losses – in particular nitrogen and sulphur.


N is lost from wet soils through two main processes

  1. Leaching below the root zone – especially in sandy soils
  3. Denitrification into the atmosphere especially on saturated clay loam and clay soils

The loss applies only to nitrate-N in wet soils. N in the ammonium or organic form is not directly affected but can be affected after it is converted to nitrate.

Wet soils result in large loss of fertilizer N, especially if:

  • Applied in early fall
  • Broadcast applied

Large losses of residual soil N from unused fertilizer, N released during full or partial fallow, manure or legumes may also occur.

N losses are dependent upon the form of N in the soil

Fertilizer N is often applied in an ammonium form (eg urea or anhydrous ammonia). Organic N (from soil organic matter, manure, and plant residues) mineralizes to the ammonium-N form through microbial activity. N in the ammonium form (NH4+) has a positive charge in the soil and is held against leaching by clay and organic matter in the soil. Hence – nitrogen in the ammonium-N form is much less vulnerable to N loss than nitrate-N. However, soil bacteria naturally convert ammonium-N to nitrate-N. This “nitrification” activity is minimized under cool fall soil conditions.

Even spring applied ammonia-form N will convert to nitrate. Recent Manitoba research indicates that conversion from ammonia to nitrate forms is driven primarily by soil temperature (Table 1). The warmer the soil, the more rapid the conversion to the vulnerable nitrate form. Therefore, time and temperature have a dramatic impact on the rate of conversion, similar to the concept of “heat units” for crop growth. For example, the amount of heat required to convert 50% of the ammonia N to nitrate is similar to that required for the emergence of corn seed – since both are biological actions.

Table 1. Nitrification rates of ammonia to nitrate form of nitrogen for banded urea (calculated from Thiessen et al, 2003)

Average soil temperature C at band depth  50% conversion to nitrate 100% converted to nitrate
Days Days
1 °C 190 380
5 °C 38 76
10 °C 19 38
15 °C 13 26
20 °C 10 20

Other factors may influence this rate of nitrification:

  • Conversion of banded anhydrous ammonia and banded urea is expected to be similar and both are slower than for broadcast fertilizer, since the high concentration of ammonia in the band temporarily inhibits microbial activity.
  • Conversion from ammonia to nitrate is interrupted or very slow when soils become saturated.

Nitrate leaching

  • Is a physical process that can occur except when soils are frozen
  • Nitrate moves with water because nitrate is water soluble and not held by soil particles (clay and organic matter)
  • Is not widespread in the Prairie region – but occurs mainly    
    1. during heavy rains or snow melt,
    3. in depressional areas of landscape and
    5. in sandy soils due to poor capacity to hold water and the ease of water infiltration and movement in sandy soils     (see Table 2)

Table 2. Effect of soil texture on depth of water penetration through saturated soil

Soil texture

Water penetration (inches into soil per inch of rain)
Clay loam 3
Sandy loam 5
Sand 10


Denitrification is mainly a biological process. This occurs when soil is wet and soil oxygen levels are low, forcing some soil bacteria to use nitrate to oxidize carbohydrates as they breakdown organic matter. Bacteria convert nitrate-N (NO3-) to nitrous oxide (N2O) and dinitrogen gases, which escape into the atmosphere. This occurs slowly in cold soils (2-4 lb/ac/day at 5oC) but rapidly in warm soil. It occurs mainly in depressional areas in clay soils after snowmelt or heavy rains.

This spring the root zone was not recharged when rains began, so a considerable amount of the rainfall could be absorbed before the soils became saturated. Below normal temperatures this spring will also have slowed this process. So denitrification losses should not have been substantial. However, if the soil remains saturated as the soil warms up, denitrification losses will continue.

Factors that Increase Losses of N in Wet Soils

Practices that lead to a high proportion of N being present in the nitrate form increase risk of denitrification and leaching losses. Such practices include:

  • use of N containing N in nitrate form already – ie ammonium nitrate (50% as nitrate) and UAN solution (25% as nitrate)
  • fall application of ammonia N forms to warm soil
  • broadcast vs banded N applications

Other practices that may increase leaching and denitrification losses are:

  • excessive accumulation of nitrates through excessive manure applications
  • early plowdown of legume forage or stubble
  • summerfallowing
  • inefficient use of water through summerfallowing
  • planting of crops – spring annuals vs. fall annuals vs. perennial crops

How much fertilizer N has been lost?

Estimating fertilizer N losses due to wet soils is complicated and not terribly accurate. Since losses are greatly dependent on whether N was in the nitrate or ammonia form, one must estimate the conversion processes. Furthermore, rainfall amounts have varied widely within Manitoba (from 6-12” since April 1 in S Manitoba). Decisions must be made on a field-by-field basis to account for rainfall amount, soil texture (which determines whether leaching or denitrification is the greatest threat) and N management practice. For example:  

  1. If urea or ammonia N was applied in fall, the conversion to nitrate was probably complete by mid to late May:
    • leaching losses on sandy soils could be high, especially in low areas, with N leached out of the root zone
    • denitrification losses on clay soils may be moderate, depressed due to the cool soil temperatures. If the soil was saturated for 10 days the losses may be:     2 lb nitrate-N/ac/day loss x 10 days = 20 lb N/ac.
  2. If urea or ammonia N was applied early spring, perhaps 50% will have converted to nitrate form – hence losses will be only a portion of that above.
  3. If urea or ammonia was banded at seeding, losses will have been minimal, regardless of soil type and rainfall amount.

Can one quantify fertilizer N losses through testing?

Soil testing in mid to late June may prove useful, but may be complicated by:

  • Ammonium and urea-N are not detected by the conventional nitrate test.
  • Banding creates areas of very high N concentration strips between low N areas and gathering a representative sample is very difficult. Many cores must be taken to overcome the banding challenge.
  • Even if the midseason soil test values are accurate, the interpretation of those values is very challenging and is not the same as interpretation of soil samples taken prior to crop establishment. The amount of soil plus fertilizer N required to feed the crop until maturity will depend greatly on the stage of crop growth and the yield potential. For example, a wheat crop takes up a large part of its nitrogen requirement between tillering and heading. Therefore, low soil test N values for an advanced crop are not as large a concern as low soil test N values for a juvenile crop.
  • It is late enough that some N will be mineralizing from organic matter. This is available to the crop – but generally not accounted for when developing N recommendations from the nitrate test.
  • Supplemental fertilizer N should be applied early enough to increase yield potential (e.g., prior to heading or bolting in cereals or canola, respectively).
  • Some areas have developed a pre-side dress nitrate-N test for corn. These have been calibrated to provide a fertilizer recommendation based on the nitrogen present. For details, refer to this Ontario webpage

Crop scouting and tissue testing

  • Scout fields carefully to note N deficiency, which is general yellowing of the young plant. Unfortunately, severe wetness and oxygen depletion of the root zone creates identical visual symptoms to N deficiency. (I’m glad that you made this point – a couple of years ago we got severe yellowing from cold and wet in some canola crops that were unrelated to N)
  • There are few N critical levels established for crops tissue sampled at this stage. For winter wheat the critical level is 4.2% N. You will need to check with your soils lab for criteria.
  • Since the plant expresses N deficiency through reduced leaf greenness, these can be detected visually or with devices such as a chlorophyll meter. However, chlorophyll meters are not widely available, need to be referenced to a “high N” check area and critical levels are only developed for Manitoba crops of winter wheat and corn.

Does it pay to apply more N to the crop?

This depends on how much N was lost and what the potential yield will be. Delayed planting or stand loss and plant stunting in the wettest areas will have reduced the yield potential, and perhaps the remaining N is adequate.

Supplemental N rates should not be based on full N loss and replacement to original application levels. For cereal and canola crops consider the following suggestions:

  • Where N losses are estimated to be high and yield potential is still good – apply up to 2/3 of original targeted N rate
  • Apply up to 1/3 of original targeted N rate if estimated losses are moderate but yield potential is good – or if estimated losses are high but potential yield is only fair.

Fortunately in the eastern Prairies spring rainfall is more reliable and so top-dressed N is often moved into the root zone of the growing crop. At this point, volatilization losses of top dressed urea may be high if rainfall is not received. Consider use of a urease inhibitor or other N forms, such as dribble banding UAN solution.


Sulphate-S (SO42-) is moderately susceptible to leaching in sandy soils. It tends to leach less than nitrate-N owing to its combining with soil calcium and forming less soluble gypsum in many soils. Losses and S deficiency will be most likely on knolls and other well-drained areas of the field. As with nitrogen, observe fields closely for signs of S deficiency – especially in canola fields. Visual S deficiency symptoms are cupping and purpling of leaves. Tissue sampling may also prove useful. Supplemental S fertilizer in the sulphate form (ammonium sulphate or ammonium thiosulphate) can be applied until the bolting stage of canola.


In summary, excess soil wetness causes several soil fertility problems, including significant nitrate-N losses by leaching and denitrification. Estimates of N losses and possible supplementation with more nitrogen is a complicated process and must be performed on a field-by-field basis.

Prepared with the assistance of:
Don Flaten, Soil Science Department, University of Manitoba
Cindy Grant, Agriculture and Agri-Food Canada