Agriculture: Cotton Pest Management Guidelines

Integrated Weed Management

Effective, economical weed control in cotton requires an integrated approach that includes cultural, mechanical, biological, and chemical methods. Controlling undesirable vegetation around field roadsides, fencerows, and ditch banks is also an integral part of an effective weed control program in cotton. These areas are prime sources of weed seed production for subsequent field infestation. Make a special effort to destroy perennial grasses, nightshades, field bindweed, and other competitive weeds in these areas.

An important component of a successful weed management program is crop rotation. Whenever the same crop is planted year after year, there is a good chance that one or more weed species will increase because they are adapted to the same conditions as the crop. Also, repeated use of the same herbicides (same mode of action) will favor increased populations of tolerant weed species. Rotating to another crop disrupts weeds adapted to cotton growing conditions and enables the use of different herbicides (different modes of action) so the tolerant weed species in cotton can be controlled. Annual weed problems can be minimized by a rotation system that includes cereals and alfalfa.


Herbicides can be used to minimize weed management costs. To reduce the need for chemical controls, select fields free of aggressive weeds such as nutsedge, field bindweed, and annual morningglory, which are difficult to control. Consider using herbicide-tolerant varieties of cotton. Herbicide-tolerant cotton varieties available to California cotton growers include Roundup Ready and Liberty Link.

To select the most effective herbicide(s), one must know the weed species present and consider the soil type, cropping sequence, and the timing of cultural operations. Records of weed infestations including weed species and their density should be kept on a field-by-field basis. Only through knowledge of the infestation can one plan an effective, economical weed control strategy.

Depending on the species and density of weeds present in a field, treatments may or may not be needed during any of the following cultural periods:

  • Preplant treatments with dinitroanilines are almost always cost-effective even with herbicide-resistant varieties.
  • Mid-season cultivation can be used to control emerging weeds.
  • If cotton stands are weak, layby treatments are especially beneficial.

Preplant-Incorporated Herbicides

These herbicides are applied to the soil surface and mechanically mixed into the soil before the crop is planted. Trash and large clods will reduce their effectiveness. Incorporate preplant-incorporated herbicides to a depth of 3 to 4 inches within 24 hours of application. Because most tillage equipment leaves the herbicide in the top half of the tilled soil, till twice the depth that herbicide placement is wanted.

Postemergence Herbicides

These herbicides are applied to emerged weeds. For effective control, apply when weeds are less than 2 inches tall. Many of the postemergence herbicides are applied as directed sprays to the base of the cotton plant to contact weed seedlings that have germinated in the row. To effectively and safely post-direct herbicides, the cotton needs to be 6 to 8 inches tall. When most postemergence herbicides contact the terminal growing point of the cotton plant, severe damage (and possibly death) may occur, causing growth retardation and delayed maturity.

Because no one herbicide controls all weeds present, herbicide combinations or sequential applications at preplant, postplant, layby, or two or three of these stages may be needed. On fallow beds carfentrazone (Shark), pyraflufen (ET), flumioxazin (Chateau), or either of these plus oxyfluorfen (Goal) are combined with either glyphosate (Roundup) or paraquat (Gramoxone Inteon) to increase efficacy on larger weeds and broaden the spectrum of weeds controlled. Prometryn (Caparol) can be combined with either trifluralin (Treflan) or pendimethalin (Prowl) and applied preplant incorporated, for control of nightshade. MSMA can be applied in combination with prometryn (Caparol) as a postdirected (post crop emergence, directed at weeds) spray for such hard-to-control weeds as nightshade. Pyrithiobac-sodium (Staple), applied over the top of cotton plants from the time the cotyledons appear to the emergence of the first true leaves, is another management option for nightshade postemergence control.

Herbicide Resistance

Herbicide-resistant weed species develop through selection pressure imposed by repeated and often continuous use of an herbicide with the same mode of action. Long-residual preemergence herbicides, or repeated application of postemergence herbicides will further increase selection pressure. Factors that can lead to or accelerate the development of herbicide resistance include weed characteristics (e.g., weeds that produce many seeds), chemical properties (e.g., herbicides with long residuals), and lack of good cultural practices (e.g., lack of tillage).


The first step in preventing herbicide resistance is early detection. Be on the lookout when monitoring for patterns that indicate resistance. These include patches of dense weed populations with less dense populations radiating out from the central patch and escapes scattered in no particular pattern throughout the field.

Prevention and Management of Herbicide-Resistant Weeds

Important weed management strategies to help prevent the development of weed resistance to herbicides or to keep herbicide-resistant weeds under control include:

  • Preirrigate, followed by tillage or herbicide applications to control emerging weeds
  • Use certified seed that is free of weed seeds
  • Rotate herbicides that have different modes of action and WSSA Group numbers (see Table 1)
  • Rotate crops
  • Monitor for weed survival after an herbicide application
  • Use nonchemical weed-control methods such as cultivation or hand weeding with a hoe
  • Use residual herbicides
  • Clean equipment after working in weed-contaminated fields
  • Control escaped weeds before they can produce seed
Table 1. Herbicides Registered for Cotton Production.1
Chemical Name Example Trade Name2 Mode of Action3 WSSA4 Group No.
carfentrazone Shark triazolinones 14
clethodim Select Max lipid biosynthesis inhibitor 1
diuron Karmex photosynthesis inhibitor 7
fluazifop-p-butyl Fusilade lipid biosynthesis inhibitor 1
flumioxazin Chateau N-phenylphthalimide 14
glyphosate Roundup amino acid synthesis inhibitor 9
metam sodium Vapam fumigant 27
MSMA MSMA organoarsenical 17
oxyfluorfen Goal diphenylethes 14
paraquat Gramoxone Inteon cell membrane disrupter 22
pendimethalin Prowl mitotic inhibitor 3
prometryn Caparol photosynthesis inhibitor 5
pyrithiobac sodium Staple amino acid synthesis inhibitor 2
pyraflufen ET phenylpyrazoles 14
s-metolachlor Dual Magnum shoot and root inhibitor 15
sethoxydim Poast lipid biosynthesis inhibitor 1
trifluralin Treflan mitotic inhibitor 3
1 Adapted from Vargas, R. And Wright, S. 2004. Cotton Field Check: A Cotton Management Update from UC Cooperative Extension-Herbicide Resistance Management.
2 Use of trade names does not constitute an endorsement by the University of California.
3 to prevent or delay the development of herbicide resistance, rotate herbicides with different modes of actions and WSSA group numbers.
4 For additional information on herbicide resistance, visit Weed Science Society of America (WSSA).


To select the most effective herbicide(s) and rotation crops, conduct surveys and keep records of weeds and how their populations are changing. Survey each field; adjacent fields can have very different weed populations as a result of cropping history or soil type. Conduct field surveys four times per growing season, once during each of the following periods: preplant to planting, crop emergence to seedling growth, early squaring, and from first open boll to preharvest. Keep records of your observations. Sampling forms.

Weed Management before Planting

Select fields that are free of perennial weeds such as nutsedge, field bindweed, bermudagrass, and johnsongrass, if possible. These weeds are usually easier to control in rotation crops (see CROP ROTATION) or during fallow periods. Laser leveling of fields will eliminate low spots where weed growth is favored. Tailwater return systems that prevent the accumulation of water at field ends will also reduce weed problems. Turn under crop and weed debris from previous crops soon after harvest to aid decomposition. Trash-free seedbeds will facilitate early cultivation and enhance herbicide incorporation and uniform stand establishment.

Conservation Tillage

In recent years, interest in conservation tillage systems has grown as a result of the increased number of herbicide-tolerant cotton varieties, higher fuel prices, access to better conservation tillage equipment, and environmental air quality issues. Conservation management plans, now required by the San Joaquin Valley Unified Air Pollution Control District, list the use of herbicide-tolerant cotton and reduction of cultivation as practices acceptable in dust reduction. The advantage of herbicide-tolerant cotton (mainly Roundup Ready) has been the ease in applying glyphosate with cotton in the field to provide effective control of weeds. Production costs decrease because growers make fewer trips across fields to apply herbicides, reduce the number of cultivations, and reduce or eliminate hand-weeding.

Conservation tillage systems are most often practiced with herbicide-tolerant cotton varieties, but conventional varieties and herbicides can also be used with conservation tillage systems. The Roundup Ready Flex system when coupled with a conservation tillage system increases the weed management flexibility. In the future, tillage and hand pulling may be needed because major weed shifts and some weed resistance is being observed in other states in cotton and similar cropping systems (corn) that use conservation tillage based on herbicides and glyphosate-only systems.

It is important to rotate glyphosate with an herbicide that has a different mode of action in order to reduce the potential for the development of weed resistance. If pyrithiobac sodium (Staple) is used in a conservation tillage system, injury to subsequent crops may be a problem. In contrast to tillage systems, not tilling the soil leaves residual herbicides such as pyrithiobac sodium undiluted in the soil profile. This may lead to injury of crops (e.g. Tomatoes) following cotton.


Winter Fallow Beds

Before establishing fallow beds, inverting the soil to the plow depth will bury problem species such as nutsedges, annual morningglory, and nightshades. Most weeds germinate in the top 1 to 1.5 inches of soil. Deep plowing with Kverneland-type plows before planting can be used to bury most seeds to prevent their germination. For weeds that do germinate, hand rogueing and removing them from the field will reduce seed production and reduce future infestations. Inverting the soil should be done infrequently to allow time for the buried seeds and tubers to decay. For nutsedges, this takes about 3 years. In some areas, deep plowing can bring salts back to the upper soil profile.

Mechanical cultivation of fallow cotton beds with the use of sectioned rolling cultivators can be effective if weeds are young. Two to three cultivations may be necessary to control weeds, depending on winter rainfall patterns. However, wet weather may prevent timely entry into the field and cultivating when soils are too wet can create soil compaction. Also, labor and fuel costs may limit the feasibility of multiple cultivations. Deferring preirrigation to late February can overcome some of these cultivation problems. Weed seedlings germinating as a result of preirrigation should be destroyed chemically or mechanically before planting the crop.

Preplant Cultivation

Cultivation just before planting controls small weed seedlings and prepares the bed for seeding. To give cotton a head start on nutsedge, use sweeps or other shallow cultivating tools to dislodge early nutsedge growth before planting. Mulching the beds also gives cotton a head start on nutsedge.


Herbicides in Winter Fallow Beds

A large percentage of fields planted to cotton using either conventional or herbicide-tolerant varieties are treated with a dinitroaniline herbicide (trifluralin or pendimethalin) and are listed or bedded up during fall and winter. For emerged broadleaf weeds not controlled by dinitroanilines (e.g., mustards), use oxyfluorfen (Goal), flumioxazin (Chateau), carfentrazone (Shark), pyraflufen (ET), or prometryn (Caparol). These herbicides can all be applied to fallow beds. To prevent damage to the cotton plants, work oxyfluorfen-treated beds with a rolling cultivator to a depth of at least 2 inches before planting to break the soil surface. Once the soil surface is broken, oxyfluorfen loses its effectiveness.

Applications of paraquat (Gramoxone) or glyphosate (Roundup) are often necessary for postemergence control of winter annual grasses and broadleaf weeds before planting. Both herbicides can be applied alone or in tank mix applications with a broadleaf herbicide. Do not spray during air inversions or when it is windy; special restrictions exist in the San Joaquin Valley as a result of past off-target movement of winter fallow bed herbicides.

Preplant Herbicides

Trifluralin (Treflan) and pendimethalin (Prowl), two dinitroaniline herbicides, are used extensively during the preplant period in cotton fields to be planted with either conventional or herbicide-tolerant varieties. These herbicides are effective against most annual grasses and many broadleaf annuals. However, weeds in the Solanaceae family (nightshade), Asteraceae family (sowthistle), and Brassicaceae family (mustards), and annual morningglory are not controlled by them. These herbicides also control seedling perennial grasses, but not regrowth from rhizomes.

Incorporate preemergence herbicides to a depth of 2 to 4 inches using an offset finishing disc with gauge wheels, springtooth harrows, rolling cultivators, or power-driven tillers. Depth of incorporation must be controlled to prevent growth retardation of the cotton plants. During planting, place the cotton seed at the lower zone of the treated soil layer for best results.

A shallow, preplant-incorporated application of trifluralin or pendimethalin is sometimes included as part of the planting operation. The herbicide is sprayed between the dirt pushers and planter, and incorporated by rolling cultivators mounted before the planter. This method, called ROCAP, provides good control when soil moisture is adequate.

A preplant treatment with the soil fumigant metam sodium can be used for control of nightshade and nutsedge. Nightshade control has been excellent; however nutsedge control is erratic on sandy soil and poor on clay loam soils. The high rates needed for good nutsedge control sometimes reduce seedling vigor. The ROCAP method and metam sodium are rarely used today for weed control.

Weed Management at Planting

To help establish a uniform and competitive stand of cotton, do not plant the crop unless the soil temperature is at least 58°F at 8:00 a.m. at the depth of seed placement. Once soil temperatures are above this threshold, plant only when a minimum of 15 degree-days are predicted for the next 5 days. For Acala cotton in the San Joaquin Valley, accumulate degree-days using a lower threshold of 60°F. Pima can be planted under slightly cooler conditions. Follow UC Cotton Planting Forecasts issued during the planting season to plant into the most optimal conditions. Proper timing of planting coupled with correct planting depth, adequate soil moisture, and fertilizer placement will ensure rapid and uniform crop emergence and seedling growth. A vigorous, uniform stand of cotton will compete with weeds more efficiently than one being established under adverse conditions.

Weed Management after Planting

Cultivation after Planting

Mechanical cultivation continues to be one of the most important methods of controlling weeds in cotton. For best results the cultivation equipment must be carefully aligned to follow the seed row precisely and as close to plants as possible. Weed seedlings are killed easily when they are small (1-2 inches in diameter); therefore, schedule cultivations before the weeds deplete soil moisture and while they are easily dislodged.

The equipment used for bedding, planting, and cultivation must be matched for row spacing and to cover the same number of rows with each pass. Effective equipment for cultivation includes sweeps, bed knives, rolling cultivators, reversed disc hillers, and rod weeders. (Sweeps and bed knives are more effective on nutsedge and grasses.) When this equipment is used individually or in combination, effective early season weed control can be achieved.

For close, in-row cultivation in cotton, a guidance system can be used. The guidance system must be used for both the planter and cultivator, and both operations must be performed in the same direction for each row.

Layby Cultivation

Timing the last cultivation just as the rows close will protect cotton yields and quality from late-season weeds if cotton grows vigorously and there are not many skips. About 5 to 10 days after an irrigation, cultivate to throw soil over weed seedlings in the drill row; this cultivation need not be as precise as earlier cultivations because cotton plants will tolerate some soil covering the stem and leaves at this time. Be sure to cultivate shallowly to avoid pruning the roots. Layby cultivation also prepares furrows for subsequent irrigation.

Hand Weeding

Hand weeding with hoes can be an important and effective means of controlling weeds within the planted row where weed removal with cultivation is difficult. It can also be a useful tool in weed resistance management by removing weeds that have survived previous herbicide applications before they produce seed. Cotton can be thinned to a desired plant number, if necessary, with early hand hoeing.

When scattered weed infestations such as velvetleaf (less than 10 in a field) and other aggressive, hard-to-control weeds are present, pull by hand and remove these plants from the field to minimize seed production and distribution. A weed like annual morningglory must be hoed before it twines. Hand weeding requires large amounts of labor that may not be available and is costly, making this method less appealing and sometimes prohibitive.

Postplant Herbicides

During the postplant period, diuron (Karmex), prometryn (Caparol), s-metolachlor (Dual Magnum), oxyfluorfen (Goal), and pyrithiobac-sodium (Staple), can be applied to provide effective control of many weed species tolerant of dinitroanilines.

When the cotton plants are 6 inches tall, directed sprays of these herbicides can be used to control small seedlings of nightshade and other resistant species. While the herbicide is directed to the row, cultivation is used for weeds in the furrow.

Sethoxydim (Poast), fluazifop-p-butyl (Fusilade), and clethodim (Select Max) are effective against most grasses, including perennials such as johnsongrass and bermudagrass. In addition, clethodim controls annual bluegrass. Effective control of annual grasses is obtained when herbicides are applied to grasses that are actively growing and less than 6 inches tall. After treatment, adequate moisture is essential to insure uptake of the herbicide as well as a vigorous and uniform stand of cotton that can compete effectively with the grasses.

Cultivating about 5 to 7 days after treatment can further enhance johnsongrass control by exposing the rhizomes to the sun. Additionally, if the soil is dry, effective control of perennial grasses can also be obtained when rhizomes are cut into short segments by discing and cross discing during land preparation.

When pyrithiobac sodium (Staple) is tank mixed with sethoxydim or clethodim, or if an application of pyrithiobac sodium is followed by a sethoxydim or clethodim application, grass control may be delayed. If pyrithiobac sodium is tank mixed with fluazifop-p-butyl or applied within 7 days of a fluazifop-p-butyl application, reduced grass control may occur.

Glyphosate (Roundup) can be applied over the top of cotton plants (from the time the cotyledons appear to the emergence of the first true leaves ) and postdirected (herbicides are applied to the base of cotton stems to target weeds smaller than cotton) to Roundup Ready varieties of cotton for the control of annual and perennial weeds. Best control is achieved when weeds are young seedlings.

With Roundup Ready Flex systems, glyphosate can be applied through layby (14th node) and beyond, which provides increased crop safety and enhances flexibility. There are no restrictions on timing of sequential applications, and there is the potential to combine insecticide or mepiquat into over-the-top applications.

With traditional, non-herbicide-tolerant varieties, glyphosate can be used as a spot treatment to control isolated infestations of perennials or applied with a hooded sprayer to control field bindweed and other persistent weeds.

The Liberty Link system uses glufosinate (Rely), which has a different mode of action than glyphosate. Glufosinate provides broad-spectrum weed control, and there are no growth stage restrictions for over-the-top applications. It can be applied to non-Liberty Link cotton with hooded sprayers or postdirected, and there are no rotational restrictions.

Layby Herbicides

Layby applications (an application at the final cultivation as the cotton closes over the furrow preventing further cultivation) of carfentrazone (Shark), pyraflufen (ET), flumioxazin (Chateau), oxyfluorfen (Goal), diuron (Karmex), prometryn (Carparol), and glufosinate (Rely) can help control existing broadleaves. Preemergence applications of s-metolachlor (Dual Magnum), diuron (Karmex), prometryn (Caparol), and oxyfluorfen (Goal) can be used to prevent the growth of nightshade, annual morningglory, groundcherry, and cocklebur when it is no longer possible to cultivate; in addition, s-metolachlor will suppress yellow nutsedge growth. The herbicides are usually applied to the furrow, as well as the bed, and incorporated with sectioned rolling cultivators. Layby applications are especially beneficial when cotton is short and the stand is poor because without such an application, weeds that escape the preplant treatment readily grow and mature with little or no competition from the cotton plant.

Preharvest Herbicides

Glyphosate can be used before harvest for control of johnsongrass, field bindweed, and annual morningglory and for the control of cotton regrowth in conventional cotton. When present at harvest, these weeds reduce the effectiveness of defoliants, reduce harvest efficiency, lower lint grades, add to the soil seed bank, and interfere with subsequent crop production.

Glyphosate can be either applied alone, as early as 8 nodes above cracked boll (NACB), or tank mixed with tribufos (Def or Folex) or thidazuron plus diuron (Ginstar). When applied alone at 8 NACB (about 40 to 50% boll opening), it can provide regrowth control in conventional (non-Roundup Ready) varieties with little to no impact on yield or fiber quality. This earlier application can also result in improved weed control as a result of greater moisture status in the weeds as opposed to a much lower moisture status at a 4 NABC defoliation treatment. When applied in combination with defoliants, continued defoliation and improved regrowth control can be achieved. Do not apply glyphosate to cotton grown for seed, because seed quality and germination percentage will be reduced, making seed undesirable or unfit for planting.

Text Updated: 05/13