Nitrogen transformations in soil: from manure to nitrate

Water & nutrients · By the Milkshed Ledger editorial team · Published 2026-11-04

Satellite image of the southern San Joaquin Valley showing green cropland, surrounding hills and the dark water of Tulare Lake — The southern San Joaquin Valley seen from orbit in 2023, with the temporarily refilled Tulare Lake. Nitrate leached from the valley's fields accumulates in the groundwater below. Image: NASA MODIS, public domain.

Nitrogen is the nutrient crops need most and the one that escapes most easily. In dairy manure it arrives mostly in forms plants cannot use directly; in the soil it is converted, step by step, into forms they can — and into forms that can leave the field as gas or as nitrate in drainage water. Understanding those steps explains why nutrient management plans count nitrogen the way they do, and why the State Water Board's 2026 order on Central Valley dairies centres on it.

The forms of nitrogen in manure

Fresh dairy manure contains nitrogen in two broad pools:

Organic nitrogen, bound in undigested feed, microbial cells and bedding. Plants cannot take it up until soil microbes break it down.
Ammonium nitrogen (NH₄⁺), mostly from urine. It is immediately available to plants, but it is also the form most easily lost to the air as ammonia.

Liquid manure from ponds is usually richer in ammonium; solid manure and composted manure are mostly organic nitrogen. Laboratory analyses of total Kjeldahl nitrogen (organic plus ammonium) and ammonium separately tell a nutrient planner how much is available now and how much will become available later.

Mineralization

Mineralization is the conversion of organic nitrogen into ammonium by soil microbes as they decompose organic matter. It depends on temperature, moisture and the material: it runs fast in warm, moist soil and slowly in cold or dry soil. Only part of the organic nitrogen in manure mineralizes in the first season; the rest is released over following years. That residual release is why fields with a long history of manure application can supply significant nitrogen even in a year when little is applied — and why ignoring it leads to over-application.

Nitrification

In well-aerated, warm soil, specialised bacteria convert ammonium first to nitrite and then to nitrate (NO₃^-). The process is usually quick in irrigated Central Valley soils in the growing season. Nitrate is the form most crops take up in the greatest quantities. It is also highly mobile: it carries a negative charge, as do most soil particles, so it is not held by the soil and moves with water.

Volatilization

Ammonium at the soil surface, especially in alkaline conditions and when manure is left on top of dry, warm soil, can be converted to ammonia gas and lost to the atmosphere. Losses are highest in the first hours and days after surface application. Incorporating manure into the soil soon after application, or applying liquid manure into irrigation water that carries it into the soil, reduces them. Ammonia is also an air-quality concern in the San Joaquin Valley because it contributes to fine particulate matter.

Denitrification

Where soil is saturated and oxygen is scarce — after heavy irrigation, in compacted layers or in poorly drained spots — bacteria use nitrate instead of oxygen and convert it to nitrogen gases: mainly harmless dinitrogen, but also nitrous oxide, a potent greenhouse gas. Denitrification removes nitrate that could otherwise leach, but it is difficult to measure and to manage deliberately, and it represents nitrogen lost to the crop.

Immobilization

When microbes decompose material that is rich in carbon and poor in nitrogen — straw, sawdust, some bedding — they take up mineral nitrogen from the soil to build their own cells. That nitrogen is temporarily unavailable to plants. It is released again later as the microbes die and decompose, so immobilization delays rather than removes nitrogen.

Leaching

Leaching is the movement of nitrate below the root zone with water that drains through the soil. It is the pathway that matters most for drinking water in the Central Valley. It happens when there is more nitrate in the soil than the crop takes up and more water than the soil can hold — for instance when manure is applied heavily before a crop is planted, when irrigation exceeds crop needs, or during winter rains on fallow ground. Once below the roots, nitrate can take years or decades to reach the water table, which is why today's groundwater partly reflects practices of the past.

What this means for a nutrient plan

A nutrient management plan is in effect a forecast of all these processes for each field:

apply nitrogen close to the time and in the amount the crop will use it, rather than in large doses at the start;
count all sources: manure and wastewater (with their ammonium and organic fractions), commercial fertiliser, nitrate in irrigation water, and the residual release from past applications;
manage irrigation so that water drains below the root zone only as much as needed to control salts;
measure removal accurately at harvest (see forage and plant tissue sampling);
check the result against soil nitrate tests at depth.

The 2013 Central Valley dairy order expresses the goal as an application-to-removal ratio of 1.4 for total nitrogen. The State Water Board's Order WQ 2026-0028 sets out a framework that will replace it with numeric land application rates tied to a nitrogen discharge limit, whole-farm nitrogen accounting and grouped fields, to be developed over the coming years (see our history of the General Order). The soil processes described here are the reason a ratio of applied to removed nitrogen can never be exactly 1: some nitrogen is always lost to air and water, and the question regulators and farmers are working through is how much is acceptable.

Sources

State Water Resources Control Board, Order WQ 2026-0028, 15 September 2026, sections I.B and III.A.
Central Valley Regional Water Quality Control Board, Order R5-2013-0122, Attachment C (nutrient management plan).
US Environmental Protection Agency, Nutrient pollution.
University of California Agriculture and Natural Resources, UC ANR nitrogen management resources.