Identifying and Dealing with Blossom End Rot

By Chris Bond
Published: November 15, 2022
Key Takeaways

Blossom end rot is the scourge of many a fruit and vegetable garden. Fortunately, finding the disease on a few of your tomatoes doesn’t mean the end of your crop.

Your first tomato of the season. You lovingly raised it from a seed or nurtured it from its seedling stage and now it is rewarding you with its prized fruit. But wait! It has a black or brown spot on the bottom of it. What kind of terrible disease has befallen your tomato plant? You also notice something similar on the sides of your peppers or your eggplants, or even your squashes. What is going on

Fear not! This very common affliction is known as blossom end rot (BER), and it does not spell doom for your plants or your season’s harvest. If left untreated, yes, yields will be affected, but it is reversible. With a few corrective measures, you will be enjoying that garden fresh salad or making that amazing sauce in no time.

Blossom end rot is a nutritional disorder that causes the tissue on the blossom end of certain fruits to rot. This affliction is most prominent in tomatoes, eggplants, peppers, pumpkins, squash, and watermelons. It is most prominent on the first fruits of the season, though it can happen well beyond that.


How Does Blossom End Rot Affect Plants?

Blossom end rot first appears as a small bruise on the bottom or side of the fruit. It then darkens and enlarges, ultimately then causing shrinkage of the entire affected portion of the fruit or it may assume a leathery appearance.

As it is a physiological affliction (a collapse of the cell membranes), pesticides are useless in treating it. Many novice gardeners think it is a fungal pathogen and try to treat it with fungicides. While it is true that the affected portions of the fruit can become host to bacteria and fungi, leading to further decay, they are not the initial cause.

The good news about blossom end rot is that it is not a communicable plant disease. One affected plant will not transfer blossom end rot to another plant, nor will one infected fruit cause another to develop it even on the same plant.

Even better news is that it is reversible and a plant that develops fruit with blossom end rot can be restored to health and produce healthy fruits within a relatively short span of time. Fruit that is already affected by blossom end rot, however, is not salvageable; it is not reversible for the individual fruits that have developed it.

Symptoms of Blossom End Rot

pepper plant with blossom end rotBlossom end rot is an abiotic condition that primarily affects fruits in the nightshade family of plants like tomatoes, peppers, and eggplants, and cucurbits like watermelons, squashes, and cucumbers.

Blossom end rot is easily identified by its sometimes large, light-to-dark, brown-to-black lesions, generally found on the bottom or lower side walls of the affected fruit. It also tends to affect a plant’s first fruits, though it can appear at any time during a plant’s maturity.


The lesion formed by blossom end rot will be dry, though it can become a moist, rotten area if not discovered before other pathogens take advantage of the weakened tissue. These sunken dark spots appear during the fruit’s development, anywhere from when it is one-quarter to half of its mature size. The spots then continue to grow in size. Fruits that have blossom end rot will ripen faster than fruits without it.

Though there are not many, there are a few other diseases of fruit that can be mistaken for blossom end rot. Buckeye rot is a fruit disease that causes a large, dark, lesion on some fruits, but its cause is phytophthora. In some instances, cucumber mosaic virus can also appear as similar to blossom end rot in cucurbits.

On peppers, spots caused by sunscald or anthracnose may at times be mistaken for blossom end rot as well. However, these lesions are lighter in color and are not as often misdiagnosed. When in doubt, take a picture or the fruit itself to your local cooperative extension or garden center for positive identification.


Causes of Blossom End Rot

cherry tomatoes with blossom end rotBlossom end rot first appears as a small bruise on the bottom or side of the fruit.

Blossom end rot can appear unexpectedly and from a variety of causes: a sudden onset of a drought, a disturbance of a plant’s root system by improper cultivation or animal pests, or mere “jumping the gun” on the planting season and transplanting when the soil is still too cold to safely do so.

Researchers have been studying and attempting to determine the causes of blossom end rot for many decades. The prevalent theories of why this happens to fruits has been that a lack of calcium during fruit development. It might not mean that there is not enough calcium in the soil, but that there are impediments to the plant absorbing and using it.

Calcium serves many roles in proper plant health. Think of it like mortar—it helps a plant with cell wall membrane stability, aids in its transport processes, and helps to extend a plant’s primary root system. A disruption in any of these functions can lead to blossom end rot.

There are many reasons why plants might not be getting the calcium they need at that crucial time. Most of these amount to some type of stress to the plant or some impediment to natural processes. Common causes that prevent calcium uptake of plants during critical times include drought conditions, high fluctuation in moisture levels of soil, or even too wet, waterlogged soils. Too much nitrogen fertilizer, excessive amounts of potassium, or magnesium and/or too low of a pH will also inhibit calcium uptake.

Root damage can interfere with nutrient uptake, especially calcium. Any interference of the respiration process will affect calcium uptake as well. In a “normal” situation, plants lose water through their leaves, and it is replaced by moisture and nutrients absorbed by the roots. It should be a perpetual cycle. Anything that inhibits this cycle can inhibit calcium uptake. Growth that occurs too quickly can also prevent developing fruit from getting the calcium they need.



Plants that are in a phase of rapid growth may not be able to take up enough calcium for both the leaves and the developing fruit when growth is occurring too quickly. Other times, calcium can be absorbed by the roots and deposited into parts of the plant where it just sits or accumulates and is not available to be used during the fruiting process. Not encouraging excessive growth can help to prevent many of these situations from occurring. Not using fertilizers high in nitrogen are the easiest way to prevent growth that can occur way too fast… or not.

There is rising evidence to suggest that a lack of available calcium during fruiting may not be the cause of blossom end rot. Some researchers contend blossom end rot is the result of other abiotic stressors such as drought, high salinity, too much light, or too much heat, which can cause cells in the fruit to die. This leads some researchers to think blossom end rot is the cause of the calcium deficiency, not the other way around. This is based on trials where calcium levels were measured in fruits that had developed blossom end rot compared to those that did not. The findings suggested that calcium levels were about the same in both groups.

Other research indicates that periods of lush growth, when plants are producing higher levels of naturally occurring plant hormones is the cause of blossom end rot. When plants are in a highly vegetative stage, they produce increased amounts of the hormone gibberellic acid (GA). This hormone allows the cells’ membranes to be more flexible so that the fruits can grow quickly. This process restricts calcium concentrations at the blossom end of the fruit. Researchers have borne this out by applying gibberellic acid to plants under stress and inducing blossom end rot.

Whether a lack of calcium causes blossom end rot, or if blossom end rot causes a lack of calcium, remains to be seen. There are, however, measures that can be taken to potentially treat, and those that can be taken to prevent the onset of blossom end rot.

How to Prevent Blossom End Rot

Young cucurbits inflicted with blossom end rot.The lesion formed by blossom end rot will be dry, though it can become a moist, rotten area if not discovered before other pathogens take advantage of the weakened tissue.

As with so many things, the best way to handle any problem is to avoid getting it to begin with. Blossom end rot is no different. Prevention is primarily handled with cultural control methods. From making sure the nutrients and pH are spot-on, managing the water, and doing some picking and pruning (to ensuring that the plant’s physiological needs are all being met) are the medley of solutions to keep your plants free from developing blossom end rot.

Take a soil test. Before even planting anything, it is important to know what the existing nutrient levels in your soil are as well as the pH. A good pH for most fruits and vegetables is between 6.3 and 6.8. Correcting imbalances before planting will help to prevent afflictions like blossom end rot. It is important to make sure nutrient levels do not exceed the recommendation for each species of fruit or vegetable. Often, an abundance of nitrogen in the form of ammonium, will prevent your plants from absorbing calcium, even if calcium is present in sufficient levels. If you do feed your crops during the growing season, avoid high nitrogen fertilizers. There is scant evidence to suggest spraying the fruits directly with calcium will prevent blossom end rot. Most research suggests any benefit is minimal and possibly anecdotal.

Proper watering is the next most critical practice to avoiding blossom end rot. Watering should be done such that it is well absorbed.

Deep waterings once or twice per week are far better for the plants than frequent, shallow waterings. Plan on at least two gallons of water per week per plant, or about one inch of water per week, once your plants are mature. The goal here is to make sure your plants do not experience any drought stress. The addition of mulch around the base of each plant can also help to both evenly regulate moisture and to conserve some as well.

Good airflow around each plant is important. The canopy may need to be thinned out or lower branches removed to achieve this. Some pruning or thinning around the mid-section may be needed as well for plants that have an abundance of leaves. The soil around the root zone should also not be disturbed. If weeds should occur near the base of these plants, the surface of the soil can be scraped with a hoe to control them but pulling them out is not recommended if it could disturb your plants’ roots. Additionally, any fruits that do appear to have blossom end rot should be immediately harvested and disposed of.

A final preventative method is to select varieties to grow at the outset that are not as prone to blossom end rot. A definitive list of varieties of all plants is not available, but there are many good starting points. With tomatoes, for instance, pear- or plum-shaped ones are much more susceptible to blossom end rot than larger slicing varieties or cherry tomatoes. Resistant cultivars of other species that are typically vulnerable to blossom end rot can often be determined by reading seed packages or descriptions in seed catalogs.

How to Treat Blossom End Rot

immature tomatoes with blossom end rotBlossom end rot tends to affect a plant’s first fruits, though it can appear at any time during a plant’s maturity.

There are no pesticides that can be used to treat blossom end rot. Because it is due to a lack of available nutrients, and not an insect or pathogen, the best course of action is to take as many preventative measures as possible to avoid getting it. If, however, it does appear on your plants, don’t fret as it doesn’t mean your whole crop is lost.

Upon discovering blossom end rot on any of your crops, first remove the affected fruits. Then, perform a soil test to see if the soil has enough available nutrients.

If nitrogen is recommended, make sure it is in the form of nitrates instead of ammonium (NO3- instead of NH4+).

If it is calcium that is needed, don’t get it from lime, as that could raise the pH too much above the ideal spot of around 6.5. Instead, use natural calcium suppliers such as bone meal, ground egg shells, clam shells, or oyster shells.

Even moisture is critical in controlling blossom end rot. Make sure your affected plants do not receive too little or too much moisture. Mulching around the base of these plants can help to retain moisture and keep them more evenly moist. If water is needed, make sure it is distributed at the soil line, preferably with a dripline. Plants should on average receive about one inch of irrigation water per week.

Some well-meaning but incorrect resources claim that a foliar spray of calcium will correct blossom end rot. This is folly; for it to be usable for the plant, calcium must be absorbed from the roots, through the stems and leaves, and into the fruit of a plant via the xylem of the stem walls. If the introduced calcium cannot be absorbed in this manner, it will not benefit a plant suffering from blossom end rot. As fruit begins to develop, the waxy, outside layer also prohibits absorption through the fruit’s walls, again making a foliar or contact spray ineffective.


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Written by Chris Bond | Certified Permaculture Designer, Nursery Technician, Nursery Professional

Profile Picture of Chris Bond

Chris Bond’s research interests are with sustainable agriculture, biological pest control, and alternative growing methods. He is a certified permaculture designer and certified nursery technician in Ohio and a certified nursery professional in New York, where he got his start in growing.

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