Pest and Pathogen Prevention in an Indoor Garden

By Eric Hopper
Published: November 27, 2019 | Last updated: May 26, 2021 05:50:01
Key Takeaways

There is an old saying: “an ounce of prevention is worth a pound of cure.” This is so true for indoor horticulturists. Preventing pathogens and pests that could destroy an otherwise healthy crop is something every indoor horticulturist should focus on, says Eric Hopper.

Using pest prevention tactics is arguably the most important step a grower can take to defend a growroom. Although using preventative methods is not a guarantee against all pest insects and pathogens, it is sure to reduce the likelihood of problems and automatically puts the grower in a better position to combat a problem if one does arise. Indoor growers should cope with pests and pathogens using prevention, identification, and treatment. Prevention is the first logical step against pest insects and pathogens.

Then, before any sort of treatment is administered, an indoor gardener must identify the problem correctly. Once the issue has been positively identified, a gardener can research and implement a treatment.


Preventing Pathogens and Pest Insects

In most cases, both pathogens and pest insects are preventable. To prevent pest insects and pathogens in an indoor garden, a horticulturist needs to understand how most insects and pathogens get introduced. In most situations, general prevention is a grower’s best defense against a pest insect or pathogen problems.

Intake Air Filtration/Air Purification

Perhaps the most common way pathogens and pests enter a garden is through the fresh air intake. Gardeners inadvertently draw pathogens and insects into their gardens from the outdoors when the conditions are right. Molds, bacteria, viruses (by way of an insect vector), and pests can easily be brought into a garden room from the outside through an unfiltered fresh air intake.


A few examples of destructive fungi that are transmitted through the air include powdery mildew, black spot, and botrytis. Under the right conditions, these opportunist fungi quickly cause problems to otherwise healthy plants and have the capacity to destroy an entire crop in a short period of time. Since the spores of these fungi are invisible to the naked eye, they are often overlooked by inexperienced indoor horticulturists. If a crop contracts one of these destructive fungi, it takes serious work to eradicate the issue entirely. As with most problems that can occur within an indoor garden, prevention is key.

(Read also: How To Perfect Your Grow Room’s Ventilation System)

By using an intake air filter, a gardener can remove many of the spores and pest insects that could end up in the growroom. High efficiency particulate arrestance (HEPA) filters offer some of the best protection against pest insects and spores. When designing a ventilation system for an indoor garden, it is important to consider filtration for two reasons. First and foremost, air filtration will greatly reduce the likelihood of pests and pathogens and should be budgeted into the ventilation system. Secondly, depending on the specific filter, the filter will alter the rate at which the fan can move air. This is important to consider because mechanical fans are rated by cubic feet per minute (CFM). Growers use a fan’s CFM rating to determine if the fan will be powerful enough to adequately exchange the air in the garden. Since filters reduce a fan’s CFM, growers must take this into consideration when designing their ventilation systems.


In addition to intake filters, air purification systems can be installed within a growroom to eliminate spores and bacteria. Air purification systems are one of the best preventative devices available to indoor horticulturists. Photocatalytic air purifiers are probably the most effective at eliminating air-borne pathogens but are more expensive.

General Cleanliness and Sanitation

An easy yet very effective preventative measure against pests and pathogens is general cleanliness. Dead or rotting plant material, used soil, and stagnant water are ideal breeding grounds for many molds and pests. In addition to keeping a tidy grow area, it is wise for a grower to clean herself before entering the growroom. It is not a good idea for a grower to enter a growroom right after visiting a friend’s garden or doing yard work. Some professional gardeners have changing rooms with designated growroom attire.


Designated clothing for indoor horticulture may sound somewhat extreme, but gardeners who understand the power of prevention tend to make the most successful growers.

Temperature and Humidity Control

Another important prevention tactic that protects against a wide variety of pathogens is proper atmospheric control. Put another way, maintaining a proper growing atmosphere will help prevent unwanted visitors. The temperature variance from the lights-on cycle to the lights-off cycle is an important factor to consider. Keeping the temperature variance between 10-15˚F from the lights-on period to the lights-off period will reduce the likelihood of condensation. This will automatically prevent many molds or fungi from having the proper environment to grow and, therefore, prevent them from ever affecting the garden. Although a vegetative room can withstand higher humidity, a general rule is maintaining a humidity level of under 60 per cent. This is especially important for the later stages of the flowering period. High humidity is a breeding ground for molds and fungi.

Identification—Monitoring for Pest Insects

As previously mentioned, positive identification is very important when dealing with pests or pathogens. Early detection and positive identification can mean the difference between a simple fix and total infestation. Yellow and blue sticky traps are great tools for monitoring an indoor garden for pest insects. Sticky traps are like fly paper in that they catch insects in a glue-like substance. These traps can be hung above the plants or set just above the soil at the base of the plants. By closely examining the sticky traps a gardener can see which pest insects are present, if any. Daily monitoring of sticky traps will help a grower identify if, what, and where a problem is occurring.

(Read also: 10 Common Marijuana Leaf Problems and How to Fix Them)

Positively Identifying the Pest Insect or Pathogen

Positively identifying the pest insect or pathogen early on is vital to stopping the problem before it’s catastrophic. When monitoring the sticky traps and the plants themselves, there are some tell-tale signs that will indicate the specific pest or pathogen a gardener may be dealing with.

Spider Mites

Spider Mites

The first sign of a spider mite problem usually shows up in the form of yellow speckling on the surface of the leaves. Closer examination of the leaf bottom will reveal clusters of spider mites and their eggs. In more extreme infestations, webbing may be found in between or on the tips of branches and leaves.

Fungus Gnats

Fungus Gnats

A tell-tale sign of a fungus gnat problem is the small, mosquito-like black or gray insects that fly around aimlessly. They are most prevalent right after watering or when the soil is disturbed.



The first sign of a thripproblem is usually the shiny streaks showing up on the surface of the leaves. The shiny trails are the areas on a leaf where the thrip larvae have been feeding. To the naked eye, thrip larvae resemble fast-moving grains of rice. The larvae can be many different colors but are generally yellowish-green.



The first sign of mealybugs is usually cotton-like, fluffy masses found in the crotches or joints of the plant. These cotton balls are clusters of slow-moving mealybugs.



The first sign of scale is typically a protective covering or bumps on the plants’ stems and stalks. The females lay eggs underneath the protective covering. After one to three weeks, the eggs hatch and the newly-hatched nymphs leave the protective covering to move around the plant and feed. Nymphs insert their piercing mouthparts into the plant and begin feeding, gradually developing their own protective covering as they turn into immobile adults.

Powdery Mildew

Powdery Mildew

Plants infected with powdery mildew look like they have been sprinkled with white flour. Powdery mildew usually starts off as small, circular spots on the leaves, but can also be found on the stems or flowers. In some cases, powdery mildew causes the leaves on a plant to twist, break, or become distorted. Eventually, the white spots spread and cover the majority of the leaf’s surface. If left untreated, powdery mildew will greatly reduce the yield and quality of the harvest.

Treatment Options

No matter how clean a grower keeps an indoor garden or how hard she tries to prevent unwanted visitors, chances are, at some point, she will have to deal with pests or pathogens. Before running out and buying an arsenal of treatments, a grower must positively identify the problem. Growers who take the time to research the pest insect or pathogen and positively identify what it is and where it is in its life cycle will have a better chance of successfully treating the problem. Once a pest insect or pathogen is positively identified, a grower can weigh his or her options for treatment.

But remember, prevention is key when it comes to pests and pathogens. Don’t let them in and you hopefully won’t need to deal with an infestation in your growroom.


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Written by Eric Hopper | Writer, Consultant, Product Tester

Profile Picture of Eric Hopper

Eric Hopper’s past experiences within the indoor gardening industry include being a hydroponic retail store manager and owner. Currently, he works as a writer, consultant and product tester for various indoor horticulture companies. His inquisitive nature keeps him busy seeking new technologies and methods that could help maximize a garden’s performance.

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