Tips on How to Prevent Root Rot and Other Rainy Season Plant Diseases

"If you're not ready, the wet season in Kenya can turn a vibrant Shamba into a graveyard of wilted crops."

Blackspot in Citrus Farming


In Kenya, the rainy season can be two-edged. Particularly in the semi-arid parts of the nation, it provides much-needed relief for parched, dry areas. On the other hand, it carries a variety of plant diseases that, if improperly controlled could ruin your crops. These include well-known problems including bacterial blights, fungal outbreaks, and root rot that virtually overnight can destroy whole fields of crops.

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From staple crops like maize, beans, and tomatoes to ornamental plants such as roses, no plant is completely safe.

The most frustrating part of all of this is that these issues are often preventable. The right techniques, strategies, and a bit of proactive care, the Kenyan farmers, horticulturists and the agronomists have been able to deal with and even thrive during the rainy season. 

If you’re a small-scale farmer in Nyeri, a flower grower in Naivasha, a fruit farmer in any part of Kenya or even a homeowner in Nairobi tending to potted plants, this guide will help you ensure your crops don’t just survive the rainy season, they’ll flourish and give you a good harvest.

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Fix Your Soil Drainage During the Rainy Season

Soil drainage is one of the most crucial elements in preventing root rot and other water-related plant diseases. From the red loam of Central Kenya to the black cotton soils of the Rift Valley, Kenyan soils are remarkably varied. One thing is true, though, everywhere: root rot results from waterlogged ground. Inappropriate drainage allows water to build up around the roots, suffocating the plants and encouraging the spread of dangerous pathogens.

1. How Can You Prevent Waterlogging During the Rainy Season?

  • Make trenches between rows: Simple V-shaped furrows between plant rows can direct extra water away from plant bases, so improving drainage and avoiding pooling of water around the roots.
  • Raising your plant beds by even just 15 cm you create a buffer zone where water is less likely to settle around the roots, so greatly lowering the risk of rot.
  • Sort Hardpan Soil: Water drains slowly from compacted soil areas. To correct this, you will have to probe further and combine in amendments like rice husks, compost, or sand to loosen the ground and enable more water movement.
  • Use drainage holes always for Potted Plants. Make sure your plants have drainage holes in the pots you use. The bottom of a container should never be able to pool water.

Pro Tip: Planting on ridges such as those used for sweet potato farming can greatly improve drainage and lower waterlogging in areas with heavy clay soils, such parts of Kisumu.

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2. Cut Back on Overwatering

Though this is not always the case, it's easy to get caught believing the rain will meet your plants' water needs. Kenya's weather can be quite erratic; some regions see just a light drizzle while others suffer torrential downpours. If you're not paying attention, this discrepancy can cause overwatering.

Rule of Smart Watering

Stay to the Finger Test: Your guide should be the top 5 cm of soil. Should the soil seem moist, extra water is not necessary. Not only does overwatering waste water, but it also raises the risk of root rot, which thrives in damp conditions.

  • Apply mulch to control moisture. Mulch derived from dry grass, straw, or coffee husks preserves the moisture balance of the soil. It keeps the soil from getting overly soggy and stops water from evaporating too rapidly.
  • Customize for microclimates: Remember that Kenya's several regions have different climates. 
  • A garden in the cool, wet highlands of Eldoret will need less water than one in the hot, dry conditions of Kitui.

Warning: If you notice yellowing leaves, don’t assume it’s because your plant is thirsty. It could be a sign of root rot caused by overwatering.  First, check the roots; then, act.

Choose crops resistant to rain (not everything survives the downpour). 

While some crops suffer in great rainfall, others are naturally more resistant to damp conditions. Choosing crops that can survive Kenya's wet season is absolutely vital if you are planting before the long rains.

3. Top Rain-Hardy Crops for Kenya

  • Kale, or sukuma wiki: Suited for the rainy season, this hardy vegetable can withstand wet feet better than its cousin, spinach.
  • Rooted arrows: Excellent for waterlogged soils, arrowroots are well-known for their ability to flourish in swampy conditions.
  • Bananas are a great crop for places with lots of rain since they flourish in regularly moist conditions.
  • Taro, nduma: Growing in waterlogged soils, this root crop is robust against the demands of the rainy season.
Downey Mildew in Grapevines


4. Avoid These in Strong Rain

  • Tomatoes are prone to blight, a fungal disease rapidly spread in damp environments.
  • Beans: A dangerous crop during the rainy season, beans rot readily in soggy ground.
  • Onions detest too much moisture and can suffer from fungal diseases in too much rain.

Pro Move: Take into account using raised bags or containers if you have to grow tomatoes in the wet season. By keeping the roots dry, these help to lower disease risk and improve drainage.

Fight Fungus Before It Starts (Once It's Here, It's Too Late)

The humid highlands of Kenya allow fungal diseases including powdery mildew, blight, and damping-off to proliferate rapidly. Fungi flourish in moist, warm surroundings, thus the rainy season is ideal for their spread.

Natural Fungus Champions

Boil chamomile flowers, let the tea cool, then mist your plants with it. Not only quite cheap but also a natural antifungal agent is this basic organic cure.

Dusting wood ashes on your plants especially on cabbages helps stop fungal growth. Ash's alkaline character creates an environment that fungus find unpleasant.

Blend three cloves of garlic, two chilies, and one liter of water will make a garlic plus chili spray. Strain the mixture then mist it over your plants. Natural fungicides abound in both garlic and chili.

Critical: Remove the infected leaves right away and burn them as soon as you find fungal infection on your plants. Compost contaminated plant matter; this will help to spread the disease.

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5. Strengthen Weak Plants With Organic Boosts During the Rainy Season

A well-fed plant is a strong plant; strong plants are more resistant to diseases including fungal infections and root rot. Synthetic fertilizers should be avoided, though, since they might make plants too soft and more vulnerable to disease. Choose instead organic remedies to boost the immunity of your plants.

Superior Immune Boosters

  • Well-rotted compost manure is high in helpful bacteria that fight soil pathogens and enhance the general condition of the ground.
  • Making your own Fermented Plant Juice (FPJ) from molasses by fermenting banana stems or stinging nettles will be Your plants get a boost in nutrients and resilience from this natural tonic.
  • Like Phosphate from Minjingu, rock dust comprises vital minerals that enable plants to develop stronger roots, so improving their resistance to rot.

Bonus: Agro-vets' seaweed extract is a fantastic means of fortifying plant leaves against fungal invasion. Your plants would benefit much from a weekly spray of seaweed extract.

6. Mulch Appropriately

Although mulch is a great tool for moisture control and soil protection, improper application can lead to mold and rot breeding ground. Selecting the appropriate type of mulch and applying it correctly becomes especially crucial during the rainy season.

Best Mulching Materials for Rainy Season

  • Choose straw or dry grass. These materials let water pass through readily while still preserving soil moisture levels. They are far better than heavier mulching materials, which under wet conditions can compact.
  • Steer clear of thick layers here. Mulching too thickly—more than 5 cm—may suffocate the roots and produce a damp environment that encourages rot. Perfect layers are thin ones.
  • Keep mulch far from stems. To stop stem rot, make sure mulching around plants keeps the material away from the stems.
  • Never use fresh leaves, sawdust, or any wet materials as mulch since they will mat down and hold too much moisture, which might encourage fungal growth.

7. Rotation of Crops and Sterilize Tools

Though forgetting is natural, tools can also be disease carriers. Every time you use a panga or jembe on healthy plants, you are spreading those germs from past use on sick ones.

Root Rot Disease


Sterilize Tools and Purify your Soil

Wipe blades with rubbing alcohol. Use rubbing alcohol to kill any pathogens by wiping your tools down. For rapid sterilization, you could alternatively briefly burn the blades over a flame.

Rotation of crops year lowers the possibility of soil-borne diseases. Avoid planting tomatoes or beans where you planted them last season. 

Solarize Infected Soil: Infected soil can be "solarized" by covering it with clear plastic for 6 weeks. The heat generated under the plastic will kill many pathogens.

Small effort with a huge payoff.

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Final Thought

Although Kenyan farmers may find great difficulty during the rainy season, it does not mean your crops will die. Better drainage, smart watering techniques, and proactive maintenance will help you to keep your plants healthy and strong even during the most heavy downpours.  Your Shamba need not sink. See your plants flourish, robust and strong by being ahead of the rain.

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