Plant Problems? Look to Your Soil Health for the Root Cause

If you've ever planted something in your garden and then watched it struggle or fail, it's really easy to blame yourself (or maybe the plants). Well, let me tell you, it probably wasn't your fault. It was a soil issue.

Soil health is absolutely critical to plant health and productivity. That means the success of your garden each season depends entirely on the soil you're growing your plants in.

Building and maintaining good garden soil for vegetables can feel so complicated. I've been gardening for 15 years, and I'm just starting to get a grasp on how this whole organic garden soil thing works. Lately, I've been deep diving into soil health, and I realized that many of the common problems we've all faced are caused by soil issues. Let's look at how you can identify three of these soil issues and then—most importantly—how you can fix them.

Bad Drainage

WHAT THIS LOOKS LIKE: Your plants wilt even though you're continuously watering. Or the leaves of your plants are turning yellow, and the stems are rotting or mildewing. The soil seems waterlogged.

Cause: Bad Soil Structure

If your garden either can't retain any moisture in the soil, or if it's holding onto way too much moisture, then you have a soil structure problem. Think about soil structure as the home for your roots, the place where they settle in. Soil structure is made of three main components: sand, clay, and silt. They're all quite different in their size and the way they interact with your plants.

Sand

Sand particles are relatively large because they're essentially tiny fragments of rock. Sand is very porous, meaning air and water just run right through it. Sandy soil doesn't retain water well. In other words, it dries out quickly, and your plants are going to be thirsty.

Clay

Clay is pretty much the opposite of sand. Clay particles are tiny, and they stick together very tightly. That makes it tough for water and air to move through clay. Clay-heavy soil is, in fact, known for its poor drainage. Plants grown in clay soil might suffocate or rot because their roots are stuck and holding too much water that should be absorbed in the soil instead. Or they might just grow to a certain point and then stop.

Silt

Silt is right in between sand and clay. The particles are medium-size, so they let water through but drain fairly quickly. Basically, silt holds water just long enough to release it to the roots of nearby plants.

The ideal soil structure is a balanced combination of all three; this is what we call loam. Loam is pure magic for your garden soil because it holds moisture but lets excess water drain so your plants don't drown.

Solution — How to Improve Soil Structure

If your garden soil could be used on a potter's bench to create a bowl, or if it reminds you of a day at the beach, then you've got some work to do on your soil structure.

The best thing you can do to improve your soil structure is to add organic matter like compost or well-aged manure. Organic matter promotes a loose, crumbly texture. It improves water-holding capacity in sandy soils and breaks up compaction in clay soils so that water and air can move through. Without organic matter, soil can become compacted and struggle to regulate water effectively.

Nutrient Deficiencies

WHAT THIS LOOKS LIKE: Your plant's leaves turn yellow or lime green, instead of a vibrant green. Your plants barely produce any flowers or fruit. The fruits turn colors or suffer from blossom end rot. The roots of your plants are malformed or don't look healthy when you pull your root crop.

Cause: Nutrient-Deprived Soil

The soil isn’t just the home for your plants—it’s also the restaurant. Your plants are eating here! And although they do make their own carbohydrates through photosynthesis, they also need nutrients from the soil to create that food and grow.

Think back to the components of soil: sand, clay, and silt. Soils made up mostly of sand and clay are typically low in nutrients, which means they can't sustain your plants over their lifetime. Silt, on the other hand, is super rich in nutrients.

The key nutrients that your plants need to grow are nitrogen, phosphorus, and potassium.

Nitrogen (N)

Nitrogen is crucial for plant growth—there’s no lush green foliage without it. A deficiency in nitrogen can lead to stunted growth and yellowing leaves.

Phosphorus (P)

Phosphorus provides the energy plants need for root development and flowering. Without sufficient phosphorus, plants may struggle to establish strong roots and produce blooms.

Potassium (K)

Potassium helps plants stay hydrated and balanced. It regulates various plant processes, including water uptake and disease resistance. A lack of potassium can make plants susceptible to diseases and result in poor fruit quality.

There are tons of other nutrients needed for healthy plant growth (including calcium, magnesium, and sulfur), but these are the main three. Even if you start off with all the right nutrients, your soil will gradually become depleted as plants pull up nutrients they need.

Solution — How to Add Nutrients to Soil

Nutrients come, believe it or not, from dead stuff—decomposed matter from plants and animals that have died. Nutrients can also come from animal manures and castings (poop), as well as natural sources like rock dust and kelp meal.

Before you add something, it's a good idea to do a soil test to check which nutrients are actually needed in your garden. Most soil tests also check your soil pH, which can affect how well your plants are able to absorb the nutrients that are present.

Here are my top ways to add nutrients to my garden soil:

1. ADD COMPOST: Routinely adding compost to your garden is a natural way to replenish the soil and feed your plants. Before planting something new, add a 1- to 2-inch layer of fresh compost to renew the nutrient base for your plants. Push compost around the base of your plants whenever they look like they could use a little extra support. I love adding mushroom compost to my raised beds, but you can also make your own compost at home from kitchen scraps and yard waste.
2. SPRINKLE EARTHWORM CASTINGS: Worm castings come from earthworms and are chock-full of nutrients and beneficial microbes. You can buy castings or make your own with a little worm composting bin.
3. INCORPORATE LEAF MOLD: This is another type of compost made from broken down leaves, and it's one of the richest things you can add to your garden. You can make your own leaf mold with leaves from your backyard.
4. ADD NATURAL SOURCES OF NUTRIENTS: Nature provides us with plenty of sources that promote healthy plant growth by releasing nutrients slowly. Natural sources for nitrogen include organic cottonseed meal, fish emulsion, and blood meal. Natural sources for phosphorus include bone meal, fish bone meal, and rock phosphate. And natural sources of potassium include kelp meal and rock dust.

Unproductive Plants

WHAT THIS LOOKS LIKE: Your plants give you a couple of leaves, an underwhelming taproot, or just a few flowers or fruit.

Cause: Lack of Activity in Soil

Adding organic amendments can provide plants with essential nutrients, but nutrients alone aren’t enough to build truly healthy soil. For plants to thrive, they need an active, diverse soil ecosystem filled with worms and beneficial microbes—bacteria, fungi, protozoa, and other tiny organisms that work their magic underground.

These lifeforms are like chefs in the underground kitchen that is your soil. They take raw ingredients (organic matter and minerals) and turn them into plant-available nutrients. Without them, your plants struggle to access the food they need.

Here are the key lifeforms that should be present in healthy soil:

Earthworms

Earthworms eat as they tunnel through your garden soil, creating pockets of air so that water and nutrients can flow through. They also leave behind a trail of earthworm castings, which are teeming with beneficial microbes.

Bacteria

Bacteria function like a blender in your soil. They're constantly breaking up organic matter into smaller and smaller pieces and turning them into nutrients your plants can absorb.

Fungi

Fungi are like the slow cookers in soil. They gradually break down bigger, tougher pieces of organic matter. They also form mycorrhizal networks that enhance root nutrient uptake for your plants. Both beneficial bacteria and fungi can even protect your plants from disease by outcompeting harmful pathogens.

There are other microorganisms like protozoa and nematodes. Together, these guys are the living, breathing, energy-giving source for all the growth that happens in an organic garden. It truly is nature's magic.

Solution — How to Add Activity to Soil

A single gram of healthy soil can contain up to 10 billion microorganisms! Unhealthy soil, however, contains very few, if any, worms or microorganisms. Here are a couple ways to add more activity to your soil:

1. INCORPORATE ORGANIC MATERIALS: Compost, compost tea, well-aged manure, leaf mold, and natural fertilizers like cottonseed meal and fish emulsion provide a food source for soil microorganisms.
2. USE MYCORRHIZAL INOCULANTS: Introducing mycorrhizal fungi to your garden can enhance plant nutrient uptake and improve soil structure. These inoculants are available in various forms and can be applied at planting time to establish beneficial fungal associations with plant roots.

Just as important as adding life is protecting the life that's already present. Here are three ways to look after the worms and microorganisms living in your garden soil:

1. AVOID BARE SOIL: Some gardeners cover exposed soil with mulch, but here at Gardenary, we prefer to use living mulch. We plant intensively so that plant matter covers bare soil, which helps moderate soil temperature and moisture levels. These plants support beneficial fungi by providing additional roots for symbiotic relationships.
2. SKIP SYNTHETIC FERTILIZERS: Excessive use of synthetic fertilizers, especially those high in phosphorus and nitrogen, can inhibit the development of mycorrhizal fungi. Opt for slow-releasing organic fertilizers and apply them sparingly to maintain a balanced nutrient supply that supports microbial health.
3. MINIMIZE SOIL DISTURBANCES: When you break up soil structure, you harm fungal networks. Reducing tilling and other disruptive soil practices can help preserve the habitat of beneficial microorganisms.

What Does Healthy Soil Look Like?

You can often tell the difference between healthy soil and unhealthy, nutrient-depleted dirt by using your senses to detect various soil health indicators. First, grab a handful of soil. Healthy soil has a softness to it. It should cling together gently but crumble easily between your fingers.

It should feel moist, not dry or soggy.

It should be dark brown or black in color (pale soil often lacks nutrients).

It should have a fresh, earthy scent (sour or chemical-like smells may indicate poor drainage or contamination).

It should include some earthworms (plus other organisms you can't see!).

If you were to dig up the rootball of a plant, you would see a healthy, well-developed root system, not just a few roots clustered near the surface.

Build Better Soil Health

Shopping at a big box store might fool you into thinking that great garden soil comes in a bag. But great soil is actually made up of three things: structure, nutrients, and activity. And you just can't buy all that from the store. You build it over time. Then, you have to maintain it.

If you have plants that are struggling, pay attention to the signs aboveground. Are you watering a lot to little effect? Are your plants just sitting there, barely growing? Does the fruit look weird or misshapen? Let these aboveground signs diagnose whether you have a structure problem, a nutrient deficiency, or a lack of soil activity.

Once you know where your soil issue lies, you can take action to fix it. You can build in good soil drainage, nutrients, and tons of beneficial microorganisms. If you solve the problem underneath your garden, you'll see the results up top totally change.

Don't give up. Building healthy soil takes time. If that sounds intimidating, don't worry. Gardenary Soil School is here for you. Inside, I’ll walk you step by step through how to test, mix, and repair your soil using natural methods.

Click on the image below to save this post for later!