Nutrient Management


Nutrient management is among the most consequential decisions that a grower makes with respect to water quality and crop productivity. Because crops do not take up fertilizer with 100% efficiency, many growers apply organic and inorganic fertility in excess of crop demand to ensure that nutrients are not limiting to their crops. While this is often an economic decision, adding excess nutrients to the crop-soil system also creates an opportunity for nutrient losses from farms into the surrounding environment. One major loss pathway for excess nutrients is via nutrient-enriched water that drains from the surface of agricultural fields or percolates beyond the root zone of the crop and into groundwater storage. Nitrogen (N) and phosphorus (P) are generally the most limiting nutrients to crop growth, and are, therefore, added in the greatest quantities by growers and most frequently the nutrient constituents of concern in agriculturally connected waterways and aquifers. When present in excess, nitrates and phosphates can create environmental problems such as eutrophication of waterways, algal blooms, and contamination of drinking water. Recent research in the Tulare Basin and Salinas Valley has found that nitrate pollution of groundwater supplies is widespread and overwhelmingly the result of the agricultural activities in the area over the past six decades. As a result of this study, new regulations on N management have been introduced and are being phased-in throughout the state. The objectives of these regulations are to maintain crop productivity while also reducing environmental pollution due to the over-application of plant nutrients.

Fortunately, managing nutrients to optimize crop growth and water quality are not mutually exclusive. Applying the Right Amount of fertility, at the Right Time, to the Right Place, in the Right Form (4Rs) is likely to maximize the amount of fertilizer that is taken up by the crop and minimize the amount of fertilizer that is wasted or lost to the environment. Since the application of fertilizers is generally one of the highest input costs in agricultural systems, this approach saves farmers money while reducing their environmental footprint in surrounding bodies of water. However, such best management practices (BMP) tend to be highly specific to the crop and environment where they are applied. Further, they involve not only management of the nutrients themselves, but also the interaction of the nutrients with water that is added to the crop-soil system (whether via irrigation or rainfall). Therefore, BMP should be governed by a few fundamental principles, but adapted to the particular cropping context where they are applied. The objective of this practice page is to outline several of the key principles for managing nutrients to maintain water quality without sacrificing crop productivity. Also included are links to resources that will assist in better understanding and implementing BMP as well as links to case studies that exemplify context-specific applications of BMP.

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Applications: Nutrient Budgeting (4Rs)

Right Amount

Budgeting is fundamental to BMP for nutrients. First, the budget must take into account the amount of nutrients a grower expects the crop to take up and, subsequently, leave the system in the crop biomass. This amount will vary among crop species as well as among levels of productivity within the same species. For example, a corn crop that yields 100 bushels/acre (5600 lbs) will export (meaning that nutrients leave the field in the harvested portion of the plant) approximately 80 lb/acre of N in the grain and 60 lb/acre of N in the stover (which is above-ground biomass that is not grain and includes stalks/stems and leaves). If the corn crop were to yield 80 bushels/acre, those numbers would be reduced by 20%. Compare that with an iceberg lettuce crop that yields 40,000 lb/acre. This will export approximately 80lb/acre of N from the field, all in the above-ground biomass (since the whole above-ground portion of the plant is harvested). How does one figure such numbers out? There is information available for prominent crops via extension services and other online tool. However, it is also possible to estimate these numbers by multiplying the concentration of a nutrient by the quantity of biomass that contains that concentration. (For example: Corn grain contains about 1.4% N at harvest. Therefore, for a 3 ton/acre crop, the amount of N leaving the field in the grain is 6000lb x 0.014 = 84lb/acre N.

In order to anticipate the amount of nutrients likely to be exported from the field in the crop biomass, a grower must consider in advance what a reasonable yield goal is for the crop s/he is growing. If the grower has had previous experience with the crop at the same location, this is often a good guide. Also, trying to get a general idea of typical yields for the crop and region in question can be an important step. This information might be gained by consulting with other growers, with a professional crop consultant, and/or a university extension agent, such as the UCANR Statewide Integrated Pest Management Program, the UC Vegetable Research and Information Center, the UC Manure Management Crop N Uptake Calculator and the UCANR Soil Fertility Management Guide for Fresh Market Tomato and Pepper Production. It is important that the yield goal not be a “yield wish”. Fertilizing for a crop yield that is not attainable in a given context (due to inherent biophysical and/or management constraints) is a very easy way to over-budget the fertility needed and create an opportunity for nutrient pollution in connected water bodies.

Click for more information about below-ground biomass

No crop will use fertilizers with 100% efficiency. In fact, 60-70% efficiency is generally as good as can be accomplished, and many of the most common crops grown in California are estimated to have much lower average efficiencies. The reasons are that 1) plants are often in competition for nutrients with the micro-biota in the soil and 2) nutrient losses via the movement of water and gas are an inherent part of a dynamic, productive biological environment. However, applied fertility that goes unused by a given crop can still be incorporated into the plant-soil system by using cover crops, rotating with crops that have distinct root systems and nutrient uptake patterns, and by other management practices that are soil building. A fertile soil with a high nutrient supplying capacity can compensate for a fertilizer deficiency in the short to medium-term. Conversely, a less fertile soil may require more applied nutrients than the above ground portion of the crop will use in order to account for the fertilizer use inefficiency and the low nutrient supplying capacity of the soil. For this reason, soil fertility testing is an important part of determining the right amount of nutrients to add. However, interpretation and application of soil tests varies greatly from crop to crop and across environments. The following Soil Fertility Testing links can be referenced for more information:

There are many tools available to budget for the fertilizer demands of different crops. Several are included on this page, and more can be found online and by talking to your university extension agent and/or a professional crop consultant.

Right Time

Pre-plant applications of fertilizer are the most common approach to nutrient management. There are both biological and logistical reasons for this. Biologically, it is important that the crop receive adequate nutrition early in its growth, when its yield potential is being determined. Logistically, pre-season applications can be accomplished in concert with seeding and/or other field operations, reducing the number of passes in a field, which saves time and energy. However, the pattern of nutrient uptake by the crop changes over the course of the season based on how big the crop is and how fast it is growing. Because the absolute demand for nutrients by the crop is small early in the season, applying enough nutrients for the entire crop at the beginning of the season results in a large portion of those nutrients being available and mobile in the soil prior to the time when the crop can take it up. As water moves through the system, these nutrients can move beyond the zone of use for the crop [whether via surface losses or downward (leaching) losses] and become a water quality concern. One way to avoid these losses is by splitting the application of fertilizers into smaller portions that are applied at key points in the development of the crop. Depending on the crop and irrigation system, there are economic and logistical limitations to how many applications are possible and warranted. Yet, even two applications can greatly improve the fertilizer use efficiency compared to a single application.

Right Place

In addition to timing and quantity, the location of fertility additions to the soil profile will determine how efficiently they are used. N can be added in ammonium, nitrate and organic forms. In the soil system, these forms are dynamic, and the vast majority of plant N uptake is in the nitrate form, which is highly mobile in the crop-soil system. The degree of N mobility depends on the soil type, the amount of soil organic matter and carbon present, and, importantly for in-season management, the degree to which the water inputs exceed the water demands of the crop. Therefore, in the irrigated cropping systems that predominate California agriculture, managing the supply of water to match crop demand is the most important tool for optimizing the placement of N in the crop-soil system (seeInteraction with Water, below). Unlike N, phosphorus in the phosphate form is generally not mobile downward through the soil profile. It can, however, be lost via the surface movement of water, particularly in soils with low P-fixing capacities or where soil sediment is lost as runoff (because P binds strongly to soil particles). More information on BMP for Phosphorus in the environment can be located here. To reduce surface losses of P, placing or incorporating P fertilizers (or organic fertilizers high in P content such as poultry manure) far enough into the soil profile that they are less likely to be lost to the horizontal movement of surface water but still available to the roots of the crop is an important measure. The optimal depth for incorporation will depend on the rooting depth(s) of a given crop at the time(s) when the demand for P is critical to its growth and development. If runoff from the crop-soil system is inevitable, establishing vegetation buffers and tailwater ponds on the borders of the cropping area can help to uptake and recycle the excess nutrients before they reach connected waterways. Grismer et al., Corkidi et al. and the USDA National Agricultural Library are other informative resources pertaining to vegetation buffers. More information on tailwater ponds can be accessed on the reuse of agricultural wastewater practice page and through the Schwankl et al. publication.

Right Form

The form of fertility will determine how quickly nutrients will become available as well as the cost of fertilizer. Because BMP for this component of the 4Rs tends to be affected not only by the crop and environmental conditions but also by local, regional and global economic conditions, an understanding of the particular types of fertilizers available in a grower’s area should be integrated into his/her crop planning process. Because of the large number of inorganic fertilizer formulations, no summary will be attempted here. However, fact sheets on the various forms of inorganic fertilizers and their management can be found here. Increasingly, slow- and control-release fertilizers are being manufactured and marketed. These fertilizers are designed to become available more gradually over the course of the season to better match crop demand, improve use efficiency, and reduce losses to the surrounding environment. However, these fertilizers cost more for the same amount of nutrition, and in the irrigated context of California, control over the availability of nutrients can generally be more precisely and inexpensively accomplished via integrated irrigation and nutrient management.

Unlike inorganic forms of fertility, organic fertilizers such as manures have more variable nutrient contents that are subject to changes over time and according to the environmental conditions. One positive aspect with respect to water quality is that nutrients from organic sources tend to be made available in a ‘slow release’ manner as decomposition gradually occurs. However, how much of the fertility will be available to the crop and when it will be available are less predictable with organic forms. As a result, some of the strategies mentioned above that increase nutrient use efficiency, such as splitting applications over the course of the season, cannot be applied with the same degree of precision using organic nutrient sources. Also, since crop production systems tend to be limited by N, organic nutrient sources are often added to meet crop N demands. However, crop demand of N is generally 10 times the demand for P, yet, in many manures, the N:P ratio is closer to 1:1 than 10:1. As a result, over-application of P and the potential for phosphate pollution is high when using manures for fertility in sufficient quantities to meet crop N demands. Likewise, when manures are applied to a field in large quantities pre-plant in order to meet crop demand for the entire season, there is much time and opportunity for losses via runoff and percolation as pulses of nutrients are released from the manure that may not match crop demand. Therefore, organic sources of fertility, and manures in particular, need to be managed with extra care.


Implementing the 4Rs for nutrient management will encourage the efficient use of applied nutrients in any cropping system. The more efficiently the cropping system uses applied nutrients, the fewer nutrients will be lost, and the better the environmental and economic outcomes will be for the grower and the surrounding environment.

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Nutrient & Irrigation Management

The majority of California’s crops are irrigated. Because the timing, placement and quantity of water affect the availability and movement of nutrients through the crop-soil system, irrigation management and nutrient management should be considered together. Over-irrigating, or adding more water than the crop demands, is a common practice because crops are often grown on fields that have heterogeneous percolation of water and irrigation systems that do not deliver water with perfect uniformity. Since water is the most limiting abiotic (non-living) factor to plant growth, over-irrigating will ensure that in-field heterogeneity is overcome and that the crop is not water-limited. However, because the movement of nutrients is facilitated by water movement, over-irrigating can also lead to nutrient loss via leaching and runoff. Nutrients that are lost from the root zone or never make it there can reduce crop productivity and/or increase fertilization requirements. Nitrates that accumulate below the rooting zone of the crop eventually accumulate in groundwater via rainfall and subsequent irrigation and become a source of pollution. Likewise, nutrients lost to runoff accumulate in waterways and disrupt the balance of river ecosystems. Therefore, managing irrigation to match crop demand will ensure not only efficient water use, but efficient nutrient use and environmental protection as well. A promising example of this is the rapidly growing use of subsurface drip irrigation in tomatoes and other irrigated crops. In such systems, (demonstrated in reports produced byTim Hartz and Hartz and Hochmuth) multiple applications of nitrogen can be easily and economically applied along with the irrigation water (known as fertigation) to match the crop demand as it changes across the season. This can result in very high nutrient use efficiency and overall productivity (pages 2-3) because the availability of the nutrients and water are synchronized with the plant demand and are available in the same location. For more information on strategies to optimize irrigation management, see the irrigation management section of this website.

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A Landowners Guide to Best Management Practices: Restoration as a Means to Treat Agricultural Runoff
This report is part of a larger effort to assist growers in meeting California water quality standards, and is intended to be a resource for landowners interested in pursuing best management practices.

Arizona BMPs and GPs
In compliance with the Arizona Environmental Quality Act of 1986, the Arizona Department of Environmental Quality has proposed rules which regulate nitrogen fertilizer use through six BMPs. These BMPs address the importance of selecting the proper amount, time and placement of nitrogen, the proper amount and timing of irrigation water and appropriate tillage practices which maximize water and nitrogen uptake by crop plants.

Beneficial Management Practices for Efficient Irrigation and Nutrient Management
In 2012-13, American Farmland Trust held focus groups with specialty crop growers in California to identify obstacles to the adoption of irrigation and nutrient beneficial management practices (BMP).

California Fertilization Guidelines
Developed by the California Department of Food and Agriculture and UC Davis, these web-based fertilization guidelines work to provide accurate, timely, efficient and effective crop nutrient information across the state, and specifically in the San Joaquin Valley, Tulare Lake Basin and in the Central Coast region, Salinas Valley.

CropManage: Online Irrigation and Nutrient Management Tool
An irrigation and nutrient management tool and blog for leafy greens developed by Michael Cahn.

Dairy Nutrient Management Field Guide
Published by Sustainable Conservation, NRCS, Western United Dairymen and the California Dairy Campaign. The purpose of the guide is to help dairies achieve efficient nutrient utilization through the production of high quality forages while meeting water quality regulations, in particular the Central Valley Regional Water Quality Control Board’s Waste Discharge Requirements (WDR).

Fertilizer Research and Education Program (FREP) Database
Since 1990, FREP has funded research on many of California’s important and environmentally sensitive cropping systems. This searchable, web-based database aims to make the wealth of information contained in FREP research projects readily available, easily understandable, and convenient for growers to implement.

Healthy Crops, Safe Water
The Healthy Crops, Safe Water initiatives being undertaken by UC Cooperative Extension and Agricultural Experiment Station partner researchers with growers in order to examine farming practices and provide options for protecting groundwater. A brief description of some projects focusing on nutrient and fertilizer research management can be found here.

Horse Owners Guide to Water Quality Protection
Produced by the Council of Bay Area Resource Conservation Districts, this guide assists horse owners and facility managers to minimize water pollution through facility design and siting, horse waste management, stormwater runoff management, pasture and paddock care, and protection of waterbodies.

Nitrate Groundwater Pollution Hazard Index
The Nitrate Groundwater Pollution Hazard Index was developed to provide information to farmers interested in voluntary management practices that reduce nitrogen contamination potential in groundwater. The index works with an overlay of soil, crop, and irrigation information. Based on the three components, an overall potential hazard number is assigned and management practices are suggested where necessary.

Nitrogen Management of Lettuce: Field Scale Lettuce
This PowerPoint presentation addresses the relationship of nitrogen fertilization and lettuce. It provides an overview of the nitrogen cycle, its importance in agricultural soils, and techniques used to increase nitrate utilization by crops; and then proceeds to summarize nitrogen management practices on field scale lettuce crops.

Nitrogen Source Reduction to Protect Groundwater Quality
This report from the State Water Resources Control Board to the California legislature focuses on Tulare Lake Basin and Salinas Valley in considering methods and associated costs for reducing nitrate leaching losses from major anthropogenic sources of nitrate loading to groundwater. Management measures and recommended practices for reducing movement of nitrate to groundwater from crop operations begin on page 18 and continue through page 68.

Nitrogen Management and Water Quality Protection
This publication by the U.C. Davis Department of Plant Sciences recommends specific practices to growers in order to limit nitrogen leaching losses.

Nutrient Management Planning Guidance for Coastal Dairies
This handbook developed by the Gold Ridge Resource Conservation District aims to aid small coastal dairies in managing nutrients on their farms. The publication is intended to provide a basic understanding of the principles and practices that inform comprehensive nutrient management planning.

Nutrient Management Goals and Management Practices for Cool-Season Vegetables Fact Sheet
Published by University of California Division of Agriculture and Natural Resources in partnership with NRCS and Farm Water Quality Planning. To be used by cool season vegetable farmers to reduce nutrient pollution, specifically nitrogen and phosphorus. Provides general management practices and goals and specific sub-goals.

Nutrient Management Goals and Management Practices for Cool-Season Vegetables

A fact sheet published by UCANR, this paper includes Management Goals and Management Practices that aid to develop a comprehensive farm plan for nutrient management on cool-season vegetable crops.

Measures To Minimize Water Quality Impairments To Surface And Ground Water
Part of the UC Pest Management Guidelines, this website outlines BMPs of pesticide management on lettuce crops.

Modules and Case Studies for the 4R Plant Nutrition Manual
This publication by the International Plant Nutrition Institute is a collection of modules and case studies centered around themes of nutrient management. Ranging in scale from a field or farm to regions or watersheds, these examples describe specific practices related to principles explained in the text of the 4R Plant Nutrition Manual, or provide background information supporting the principles.

Solution Center for Nutrient Management
This website was created to increase access to California agricultural nutrient management resources and serve as a platform for conversations on important nutrient management issues. It contains resources, a research data base, farmer profiles, a discussion forum and more. This website is hosted by the University of California Sustainable Agriculture, Research and Education Program.

UCCE Agricultural Water Quality and Research Education Program
The Agricultural Water Quality Research and Education Program assists growers and the general public by researching and developing farming practices that protect water quality, and fostering the implementation of these practices in the field.

USDA Agricultural Environmental Management
This important resource, which is part of the Water Quality Information Center, is a suject-specific database cataloging studies, resources and other articles from around the country focused on agricultural environmental management.

USDA Nutrient and Pest Management
This website provides an overview of nutrient and pest management and provides a comprehensive list of other online tools and resources.

Vegetable Production Best Management Practices to Minimize Nutrient Loss
Nutrient loss from commercial vegetable fields has become a significant environmental issue in all the major vegetable-producing regions of the United States. This paper discusses five practical, low-cost nutrient best management practices (BMPs). These BMPs are widely applicable, relatively inexpensive to implement, and can radically reduce nitrogen and phosphorus loss from vegetable fields.

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Case Studies

Agricultural management practices to reduce phosphorus in the Salton Sea watershed

In the Salton Sea Watershed, approximately one-third of applied irrigation water leaves irrigated fields as surface runoff and subsurface drainage and enters the Salton Sea. Excessive loads of nutrients (mainly phosphorus and nitrogen) in Imperial Valley rivers and agriculture drains contribute to the eutrophic conditions that impair the Salton Sea. Irrigation water management and runoff reduction are two techniques used in order to comply with the TMDL levels established for the river basin and reduce the concentration and load of P runoff waters. Information on the UCCE Imperial Valley study and its corresponding recommendations can be found here.

Cox Ranch

Cox Ranch, the 155 acre property along the San Joaquin River, has utilized multiple funding sources, (including an EWP conservation easement and the U.S. Fish and Wildlife Service’s Partners for Wildlife Program) to design and construct a treatment and conveyance system to deliver water between the wetland, upland, and riparian habitats. During its first year of operation, the property has effectively demonstrated its ability to remove silt from the tail water. This case study is found on page 21 of A Landowners Guide to Best Management Practices: Restoration as a Means to Treat Agricultural Runoff Report,a report part of a larger effort to assist growers in meeting California water quality standards, and intended to be a resource for landowners interested in pursuing best management practices.

Marshall Road Drain

The Marshall Drain Project stems from the “Stanislaus County Regional Drainage Water Management Program”: This collaborative program was established by local irrigation districts to address water quality and water use efficiency in southwest Stanislaus County. The Marshall Drain was designed to remove silt and all other harmful constituents from the tailwater and recycle the treated tailwater for irrigation, thereby not allowing said constituents to enter the San Joaquin River. This case study is found on page 25 of A Landowners Guide to Best Management Practices: Restoration as a Means to Treat Agricultural Runoff Report, a report part of a larger effort to assist growers in meeting California water quality standards, and intended to be a resource for landowners interested in pursuing best management practices.

Using less fertilizer more often can reduce nitrate leaching: a case study in avocado

This study conducted near Corona, CA finds fertilizing avocado trees in smaller amounts more frequently can reduce nitrate leaching into the soil and thereby decrease contamination of groundwater.

Wingsetter Wetland Ranch

After ten years of restoration and management, Mickey Saso, the owner of Wingsetter Wetland Rach has created a collection of ponds, meandering swales, and sedimentation basins that effectively treats agricultural drainage and supports an abundance of wildlife. The 150-acre ranch is immediately west of the San Joaquin River (just north of the Merced County line), intercepting and treating the tailwater of 3,000 to 4,000 acres of upstream farmland. This case study is found on page 14 of A Landowners Guide to Best Management Practices: Restoration as a Means to Treat Agricultural Runoff Report, a report part of a larger effort to assist growers in meeting California water quality standards, and intended to be a resource for landowners interested in pursuing best management practices.

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Page Credit

Content for this page was originally developed by Dr. Mark Lundy, UC Cooperative Extension. Various others have since contributed content.