Do Synthetic Fertilizers Harm the Soil?

Healthy soil is a gardener’s most valuable resource, but certain products can disrupt the natural belowground ecology. If you are concerned about synthetic fertilizers harming your soil, here is what to look out for, explained by a soil expert and former farmer.

Close-up of a gardener's hand in a blue glove pouring synthetic fertilizers onto a plant with large succulent green leaves in the garden. The plant forms a rosette of large, strong, vertical, succulent green leaves with reddish and pointed tips. Fertilizers are granular and white.


Healthy soil is your most essential garden resource, but you might be harming your soil if you regularly apply synthetic fertilizers. These products can degrade quality, harm beneficial microorganisms, cause nutrient leaching, and lead to a buildup of salts, ultimately harming your plants.

Chemical or synthetic fertilizers contain manmade materials and petroleum rather than naturally-occurring organic compounds. For example, most synthetic nitrogen fertilizers come from ammonium nitrate or urea. These are synthesized in a lab using the Haber-Bosch process. This energy-intensive lab reaction is the same method that was used in World War I and II to manufacture nitrogen bombs. The boom of the synthetic nitrogen industry poured into agriculture around the time of the Industrial Revolution. It has since made its way into gardening products.

While synthetic fertilizers may not pose the same risks as chemical pesticides, it is helpful to know how they’re affecting your garden. Here is everything you need to know to make an informed decision, and some potential alternatives for healthier soil.

The Short Answer

Close-up of a gardener's hand throwing a pile of granular fertilizer into the air against a blurred background of a green, sunny garden. Granular fertilizers are tiny, round, dark brown balls.
Chemical fertilizers disrupt soil health, harming biodiversity and waterways.

Excessive use of chemical fertilizers degrades the soil over time. This disrupts microorganisms and causes compaction, nitrogen leaching, and loss of organic matter. These are major issues in large-scale industrial farming, where synthetic fertilizers are consistently applied over years of growing. 

However, a small amount of synthetic fertilizer is unlikely to severely harm your garden. Still, organic gardeners should avoid synthetic fertilizers if they want to promote healthy soil and build a self-sustaining garden ecosystem. Organic fertilizers like compost, manure, fish meal, and feather meal benefit soil microbes by improving biodiversity, organic matter, aeration, and natural plant-microbe interactions belowground.

Unfortunately, inorganic or quick-release nutrients can have the opposite effect. The harmful effects of synthetic fertilizers include:

Soil Degradation

Chemical nutrients can compact soil by decreasing aeration and reducing permeability, making it harder for plant roots to dig in.

Salt Accumulation

Constant use of synthetic fertilizers leads to a concentration of mineral salts that can harm plants.

Loss of Natural Fertility

Although quick-release fertilizers provide a rapid boost of nutrients for plants, they decrease fertility over time because they exhaust soil microbes, leaving them without “food” to decompose.

Reduced Biodiversity

Chemical fertilizers reduce the diversity of beneficial microbes.

Environmental Damage and Leaching

Synthetic nitrogen can leach into waterways, causing algal blooms, harm to aquatic life, and contaminated drinking water.

The Long Answer

Close-up of a gardener's hand in a white glove applying granular fertilizer in the garden. Fertilizers are granular, in irregular oval and round shapes, and have a delicate pink-apricot tint. The soil is loose and dark brown in color.
Soil ecology awareness diminishes reliance on synthetic fertilizers.

Understanding your soil can reward you tremendously. Healthy soil can increase yields, improve plant health, reduce risks of plant diseases, and improve the nutrient density of your food. Most relevant to this topic is that it can reduce the need to apply fertilizer.

Soil is a lot more complex than we think. It’s not just a bunch of dirt, but rather, a living, breathing ecosystem full of microscopic organisms. These organisms form the backbone of our garden and our planet. Without soil microbes, we would not have plants, which means we would not have food. 

Taking care of invisible organisms like fungi and bacteria is the first step to building the healthiest garden possible. For humans, a healthy diet usually involves removing junk food. A healthy garden ecology includes removing synthetic fertilizers. Here’s why:

Organic vs. Synthetic Fertilizers

Until about a century ago, all the fertilizers on Earth were natural. Gardens and farms were fueled by the decomposition of organic matter like animal manure and dead plant byproducts. In contrast, inorganic or synthetic are very new in the grand scheme of humanity.

These lab-made chemical nutrients do not contain carbon and are not permitted in organic agriculture. Ingredients like ammonium nitrate, urea, and superphosphate are considered synthetic fertilizers and are not suitable for organic gardening.

What Does Organic Really Mean?

Close-up of a gardener's hands in a dirty white glove applying organic fertilizer to a garden bed with strawberries. A gardener applies fertilizer using a garden trowel. Fertilizers have a fine, sandy texture and a light gray tint.
“Organic” denotes carbon-based materials, crucial in sustainable agriculture.

In scientific terms, “organic” means anything that contains carbon. Anything on Earth that was previously living (including poop, blood, bones, feathers, wood, and leaves) is made of carbon; thus it is organic. 

The term “organic agriculture” takes this a step further by referencing a type of gardening and farming. In the United States, organics is regulated by the USDA National Organic Program. It creates legislation and manages the certification of organic farmers. They also work with the Organic Materials Review Institute (OMRI) to label agricultural and landscape products as organic.

If you see the OMRI seal on a bag of fertilizer at the garden store, you know that it is made of natural materials and safe to use in your organic garden. Other countries have their own organic certifying agencies to label which products are truly organic.

What Does Synthetic Really Mean?

Close-up of a bucket full of blue chemical fertilizer in granular format. A bucket stands on green grass in the garden. A man's hand shows granular fertilizer by placing his hand halfway into a bucket. Fertilizers are blue in color and have a round shape.
Opting for organic fertilizers ensures quality and environmental sustainability.

Synthetic fertilizers are not always labeled as “synthetic”. However, they never contain the OMRI label because they are not legally allowed to be used in organic farming. Gardeners, of course, are not held to the standards of Certified Organic producers, but many prefer to follow organic guidelines to ensure that the food they grow is of equal or higher quality to the organic food purchased in grocery stores.

Quick-release chemical fertilizers did not exist until the early 1900s when German and American chemists began synthesizing nitrogen and, to a lesser extent, potassium and phosphate fertilizers. The rise of synthetic fertilizers was the key to the Industrial Revolution or so-called “Green Revolution” of agriculture, when large-scale machinery, monocultures, pesticides, and synthetic fertilizers replaced traditional methods for growing food.

In summary, organic fertilizers come from nature, and synthetic fertilizers come from petroleum or lab-based synthesis. Now that you understand the differences between these two types, here are the major drawbacks to using synthetic fertilizers and how they can harm your soil.

Loss of Natural Fertility

Close-up of young seedling sprinkled with granular fertilizers. The seedlings have vertical stems with several pairs of oval serrated green leaves. Fertilizers are granular, irregularly shaped, light pink in color.
Build soil health for a thriving garden without synthetic fertilizers.

Healthy soil can naturally provide all the nutrients that plants need to grow without applying any fertilizer. Think about it: old-growth redwood forests and vast wild grasslands have never had any fertilizer applied to them, yet they grow prolifically with only the minerals and nutrients that are naturally available. 

The Soil Microbiome

This is possible because of the soil microbiome, which is a complex, interconnected ecosystem of below-ground organisms, including bacteria, fungi, protozoa, and nematodes. This network of organisms is like an all-natural fertilizer cycle that slowly releases to plant root zones over time.

Inorganic fertilizers tend to be quick-release, meaning they temporarily boost plant-available nutrients, but they actually decrease them over time. The salts from chemical fertilizers make it difficult for healthy microbes to stick around in your soil, which means your garden won’t be able to produce its own “natural” fertility. 

This problem requires a basic understanding of the soil food web and nutrient cycling. Essentially, the soil is full of an entire ecosystem of organisms that work to transform dead stuff (leaves, woodchips, animal poop, blood, etc.) into plant-available forms. Plants cannot instantly uptake the nitrogen from manure, for example, because it must first be transformed by bacteria. 

Similarly, plants cannot readily absorb nitrogen from the atmosphere. The nitrogen must “pass-through” a middleman microbe called Rhizobium bacteria. These are a specialized type of bacteria that live in the roots of legumes, allowing plants like peas and beans to enrich the soil with more nitrogen. The peas don’t naturally contain nitrogen; it’s their symbiotic relationship with nitrogen-fixing bacteria that makes the natural fertilizer possible. 

Because synthetic fertilizers fill the ground with salts that harm microbes, they ultimately create a sort of “chemical treadmill” where your garden becomes dependent on them. A few doses won’t necessarily hurt anything, but regular applications can deplete your soil’s natural nutrient reserves. 

If you want your garden to be more resilient and operate with fewer external inputs, then avoid synthetic products.

Synthetic Fertilizers Kill Beneficial Microbes

Close-up of a woman's hand applying granular fertilizer in a garden. The soil is moist, dark brown. Fertilizers are round granules of bright white color.
Choose organic fertilizers to protect your garden’s natural defense system.

Chemical fertilizers don’t only harm nutrient cycling; they can also hurt the microorganisms that help your plants defend themselves against pathogens. It’s helpful to think of microbes as your plants’ natural “defense army.” For example, research shows that beneficial soil bacteria produce antibiotics that protect plants from pathogens. In other words, the “good guy” bacteria protect your plants from the “bad guy” disease-causing organisms, much like the immune system in your body.

In addition to disease protection, a higher diversity of microorganisms is correlated with higher-yielding crops and a more resilient garden. All of these benefits are disrupted when synthetic fertilizers are applied. Why? Because chemical nutrients reduce the overall diversity of soil microbes, killing off large amounts of important (yet invisible) species.

Studies show that repeated applications of chemical fertilizers can make pathogenic organisms more dominant in the soil. These products throw off the natural balance of microbes, making your plants more susceptible to disease. In contrast, organic fertilizers increase the below- ground biodiversity and contribute to plant disease resistance. So if you want to promote a healthy soil ecosystem with natural immunity, you should avoid synthetic products.


Close-up of woman's hands holding compacted dirt. It is dense and tightly packed, lacking in proper aeration and drainage. The soil is light brown.
Soil compaction worsens with chemical fertilizers, hindering plant growth.

Synthetic fertilizers are scientifically proven to worsen soil compaction. Compacted beds make it very difficult to garden, especially if you have heavy clay that turns to a concrete-like consistency when dry. If you’ve ever tried digging a shovel into soil that went “ping” when you hit it, you know how troublesome compacted ground can be. 

Salt buildup is the primary reason chemical fertilizers cause compaction. Mineral salts alter the physical structure of the soil, reducing its ability to hold onto water and air. The pockets of air between particles are called pores. They provide a space for water, oxygen, and beneficial microorganisms to hang out while nurturing your plant roots.

Without pore space, the soil becomes hardened and rough, making it difficult for plants to dig deeper in the ground. Using tillage and chemical fertilizers significantly reduces the amount of pore space, creating a hard, compressed layer that is problematic for crops and gardeners alike.

Compacted soil is closely linked to issues like root rot and other fungal pathogens. When there is a lack of air space between the soil particles, the dirt can become waterlogged and soggy. The excessively wet, low-airflow conditions create a breeding ground for pathogenic fungi that infect your plant roots. Combine this issue with the aforementioned negative impacts on soil microbes, and you can see how synthetic fertilizers have a compounding negative effect on soil ecology.

Improving Compacted Soil

If you want to combat compaction and make your soil fluffier for easier plant growth, you should add organic matter. Compost, manure, and leaf mulch are some popular sources of organic matter that contribute to nutrients and soil structure. As these materials break down, they prevent compaction and help transform your soil into the loamy, rich dirt that feels good to plunge your hands in. 

Fertilizer Burn

Close-up of pumpkin leaves burn due to excessive chemical fertilizer. The leaves develop yellow or brown scorched edges, which progress to necrosis and curling. The leaves are large, wide, rounded, dark green in color.
Excessive synthetic fertilizer can harm plants, causing severe damage.

Overfertilization is a huge problem with synthetic fertilizers. Applying too many nutrients can “burn” your plants, causing symptoms like yellow or brown leaves, wilting, and rotten or dead roots. Young plants can completely die from excessive fertilization. Once again, this issue goes back to the salt buildup caused by chemical products. The salts literally burn the plant roots, making it impossible for them to uptake the water they need to survive. 

You can avoid harming your plants by using synthetic fertilizer very sparingly, in small amounts, or avoiding it altogether in favor of slow-release options. If you accidentally apply too much fertilizer, you may need to scoop out visible granules, flush the soil profile with lots of water, or transplant the plant to a new bed or container.

Water Contamination

Close-up of a watering can pouring water on the snowdrop flowers. Snowdrops are charming early spring bulbs with a distinctive appearance. Emerging from basal clumps of slender, strap-like green leaves, each plant produces a single, nodding flower on a slender stem. The delicate blooms feature three small, white tepals surrounding a central green mark.
Synthetic fertilizers leach, creating harmful dead zones in waterways.

The final major way that synthetic fertilizers harm soil is through leaching. You may be familiar with the Dead Zone in the Gulf of Mexico. This massive area of ocean is devoid of life and oxygen because of the nutrients leaching from fertilizers. 

When we regularly apply synthetic nitrogen to the land, there is often excess nitrogen that plants cannot uptake. Rain and irrigation water send the nitrogen down into the ground, contaminating the aquifers, streams, and rivers. As these water sources feed into the Mississippi River, the nitrates flow toward the Gulf. 

When synthetic nitrogen reaches a large concentration in a waterway, it causes an overgrowth of algae. These algal blooms develop rapidly and suck up all the oxygen from beneath them, creating areas where fish and wildlife can no longer live. These “dead zones” have terrible ecological repercussions. This is easily avoidable if we use less fertilizer and prioritize slow-release organic options.

Quick-release fertilizers are particularly prone to leaching because they are water-soluble and highly mobile in the soil. This means a hard rain can easily wash them out of your garden into the groundwater below. While your garden is much smaller than the industrial farms of the Midwest, you can still have a positive impact by preventing chemical leaching. The changes will be especially noticeable if you have a small creek, river, or pond that runs near your land. As nutrient leaching is reduced and synthetic fertilizers are filtered through the soil, plant and animal life can begin returning to an area. Slow-release products are a better option because they are not as water soluble and, therefore, less prone to leaching.

Final Thoughts

In summary, chemical fertilizers certainly harm soil, especially the beneficial microorganisms that help build a self-sustaining garden. While synthetic nutrients may provide a quick boost of growth for container plants or outdoor beds, be wary of the potential impacts they can have on long-term soil health. 

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