How to Grow Hydroponic Microgreens: Complete Guide

January 26, 2024

This comprehensive guide will take you through the entire process of growing hydroponic microgreens. From setting up your system to harvesting and beyond. 

Disclosure: Some of the links in this article may be affiliate links, which can provide a small commission to me at no cost to you if you decide to make a purchase. You can read more in my disclaimer here

The hydroponic method is a great way to increase the nutritional value of your meals and up the ante on your health. It’s also an easy way to grow your own microgreens if you have limited space. 

These tiny, nutrient-packed greens are not only delicious but also incredibly easy to cultivate in a hydroponic system. You’ll learn everything you need to know in this step-by-step guide.

So if you’re looking to explore the wonderful world of hydroponics, this guide is for you. It will provide you with the knowledge and skills needed to grow nourishing, fresh microgreens right in your own home. 

Microgreens are young, edible plants that are harvested at an early growth stage. This is when you can see their ‘seed’ leaves start to pop out just before they grow in full. 

These tiny, tender greens are typically 1-3 inches tall and are often used as a garnish, salad ingredient, or culinary accent. Specifically for their vibrant colors, intense flavors, and nutrient density. 

Microgreens seeds are relatively easy to grow at home and can be grown indoors or outdoors. Either in soil or in a hydroponic setup. 

These powerful greens typically germinate within a few days and are ready to harvest within 7-21 days. Depending on the type of microgreens you choose to grow.

Microgreens have gained popularity in recent years due to their nutritional benefits, with good reason. They are packed with nutrient-rich vitamins, and minerals as well as antioxidants. And are also a great anti-inflammatory source.

You don't have to be 'extreme' to get results, just be consistent with healthy lifestyle habits.

Benefits of Growing Microgreens Hydroponically

Hydroponic growing has amazing health benefits and with the perfect kit, you’ll have your own micro greens in no time!

4 Benefits Include:

1. Growing them in a controlled environment, reduces pesticide and chemical exposure. As well as the need for harmful chemicals. Plus, fewer pests, and diseases, and less weeding!

2. Hydroponic systems enable precise nutrient control. Resulting in even more nutrient-dense microgreens. The best part is, that you can grow them all year round regardless of the season. Making them easily accessible during the colder months!

3. Hydroponics reduces soil-borne pathogens and is highly water-efficient, crucial in regions with water scarcity. 

Customized nutrient profiles can optimize microgreen nutrition, while faster growth means quicker access to fresh, nutritious greens. 

4. You can grow these hydroponic microgreens in limited spaces, making them accessible to urban living. These benefits collectively enhance the quality, safety, and accessibility of nutrient-rich microgreens in your diet.


Let’s Get Started!

Supplies and Equipment 

Before you get started, you will need to gather up your supplies for the clean soil-free growing of microgreens. 

Here’s what you will need:

Growing trays: Choose shallow trays or flats with drainage holes. These will serve as the containers for growing your microgreens. These eco-compostable growing trays are a great option.

Growing medium: Hydroponic microgreens thrive in a soil-free growing medium. Consider a grow medium using coco coir, jute mats, micro, or hemp mats for an eco-friendly alternative. These growing pads provide excellent support for your microgreen plant roots while maintaining proper moisture levels. 

Seeds: Select high-quality microgreen seeds from reputable sources such as True Leaf Market. They are my go-to and top pick for all seeds and supplies. Some of the best microgreens include sunflower, broccoli, kale, beet, and pea shoots. Arugula is another popular option. 

Spray bottle: Hydroponic systems require consistent clean water delivery. For a high-level setup, you can choose from drip systems, or flood and drain systems. However, a simple hand-watering method will work just as well. 

Light source: Adequate lighting is essential for growing healthy microgreens. You can use your sunny windowsill for natural sunlight if you live in a well-lit space. Otherwise, artificial lighting like fluorescent or LED grow lights will do the job. 

This Hydroponic Kit was the I used when I grew my first batch of microgreens and it was totally worth it. Especially if this is all new to you. 

Choosing the Right Microgreen Varieties

Not all microgreens are created equal. There are different types of microgreens to choose from for growing your hydroponic crops. 

Consider the following when selecting your microgreen varieties:

  • Taste Preferences: Choose microgreens that you and your family enjoy. Experiment with different flavors and textures to find your favorites.

  • Growth Time: Microgreens have varying growth times and typically range from 7 to 21 days. Decide whether you prefer faster-growing varieties for quick harvests or slower-growing ones for prolonged cultivation.

  • Nutritional Value: Different microgreens offer varying nutrients, vitamins, and minerals. Some are rich in vitamins, while others are packed with antioxidants and so on. 

    I would recommend getting a good variety of seeds for optimum nutrition. A good variety includes broccoli, kale, kohlrabi, radish, sunflower, and pea shoots. 

Setting up Your Hydroponic System

Now that you have your supplies and chosen microgreen varieties, it’s time to set up your hydroponic system. 

7 Basic Setup Steps

  1. Choose a Location: Find a suitable location for your hydroponic setup and optimal growing conditions. Ensure it has access to direct sunlight or power (for lighting). As well as a stable surface to place your grow tray (or trays).

  2. Assemble Your Growing Trays: Place your individual trays on a level surface. Ensure they are clean and sanitized before use.

  3. Prepare the Growing Medium: Fill your trays with the chosen growing medium, leaving about 1/2″ of space below the rim. Moisten the grow mat without over-saturating it.

  4. Sow the Seeds: Evenly spread enough seeds over the moistened growing medium. Follow the recommended seeding density for your chosen varieties.

  5. Cover and Germinate: Gently press the seeds into the medium and cover them with a thin layer of growing medium or a humidity dome. This helps create the ideal conditions for seed germination.

  6. Set Up Lighting: If you’re using artificial lights, position them at the appropriate distance above your trays. Then, set the light timer according to your seeds’ light requirements.

  7. Add Water: Spray the growing medium with enough water to ensure consistent moisture for your microgreens. Follow the seed instructions to know just how much water to add for the desired microgreen seeds. 

Preparing Your Growing Environment

Creating the perfect environment for your hydroponic microgreens is essential for vibrant and healthy growth. In this section, we’ll explore the key considerations when preparing your growing environment.

Location and Space

Selecting the right location with adequate space for your hydroponic microgreen setup is the foundation of their success. 

Whether you opt for an indoor or outdoor space, ensure it has easy access to power for lighting. You also want to ensure you place your trays on a stable surface. This will make for an ideal environment for your hydroponic microgreens to flourish.

Sanitation and cleanliness

Hygiene and cleanliness are vital in hydroponic microgreen cultivation to prevent contamination and disease.

You’ll also want to clean and disinfect your growing trays, containers, and equipment before and after each planting cycle. 

This will help prevent potential harmful pathogens from affecting your microgreens. 

It’s equally important to wash your hands thoroughly and use sanitized tools when handling your microgreens. Especially during harvest and maintenance. 

Furthermore, you’ll want to ensure you use filtered or purified water in your hydroponic system to keep it free from contaminants. 

Planting and Germination

Now that you’ve set up your hydroponic microgreen system and created the perfect growing environment, it’s time to dive into the exciting process of planting and germinating your microgreens. 

This is where the magic begins. 

Preparing the Growing Trays

Your choice of growing trays and their preparation plays a crucial role in the overall success of your hydroponic microgreens. 

Here’s what you need to do:

Cleanliness is Key: Ensure that your growing trays are clean and free from any contaminants or residue from previous crops. A mixture of water and hydrogen peroxide (1:10) can be used to sanitize trays thoroughly.

Drainage: Ensure that your trays have proper drainage. Excess water should be able to flow out to prevent waterlogged roots. Elevate one end of the tray slightly to encourage drainage.

Spacing: Depending on your chosen microgreen varieties, plan the spacing accordingly. Generally, microgreens are sown densely but not overcrowded.

Sowing the Seeds

When sowing seeds for hydroponic microgreens, follow the recommendations for your chosen varieties. It should cover the following.

Seed Density: You’ll want to try and evenly space out the seeds without overlapping. For small seeds like basil, you can use a shaker or your fingers to spread them out.

Pressing Seeds: Gently press the seeds into the growing medium using a flat tool or the back of your hand. This ensures good seed-to-medium contact, which is important for germination.

Covering the Seeds (Optional): Some microgreens benefit from a thin layer of growing medium placed over the seeds. This can help keep them in place and maintain moisture levels. However, not all varieties require covering.

If you get the hydroponic kit, you’ll have all you need to grow your microgreens successfully. Including a laminated step-by-step image card and pH Testing Kit to test the pH of your water. 

Watering and Moisture Management

Proper watering and moisture management are essential for germination and early growth stages. After sowing, gently water them using a spray bottle to ensure even moisture without over-soaking the growing medium.

Additionally, check the moisture level daily and water as needed. It’s preferable to use a spray bottle to avoid disturbing the delicate seeds and seedlings.

Germination and Initial Growth

The germination period is a critical phase in microgreen cultivation. During this phase, germination times may vary depending on the microgreen variety. It can be anywhere from 2 to 7 days. Monitor your trays closely throughout this period. 

Once the seeds have sprouted, make sure they get enough sunlight. If you’re using artificial lights, position them 2-4 inches above the seedlings. 

Maintain a careful watering schedule, to ensure the growing medium remains consistently moist. Be careful not to over-water them. Doing so will hinder their growth. 

Nutrient Solution and Feeding

Understanding Hydroponic Nutrients

Hydroponic systems rely on nutrient solutions to provide all the vital elements they need for healthy growth. 

Unlike traditional soil-based cultivation, hydroponic microgreens rely on nutrient-rich solutions. This is so they can obtain nutrients like nitrogen, phosphorus, potassium, and other micronutrients. 

The controlled environment of hydroponics allows for precise nutrient delivery, resulting in faster growth and nutrient-dense microgreens. Properly balanced hydroponic nutrients help microgreens achieve their full potential. From flavor to texture, to nutritional value, making them a vital component of the cultivation process.

Mixing and Preparing the Nutrient Solution

To mix the perfect nutrient solution, follow the guidelines provided by the manufacturer and adjust the pH level as necessary. You’ll want to ensure that your microgreens receive the right balance of nutrients for healthy growth.

If you opt for the pH Control Kit, it will make it easier to maintain a healthy pH. 

Feeding Schedule and Monitoring

Establish a consistent feeding schedule based on the growth stage of your microgreens. Monitor the EC (electrical conductivity) and pH levels regularly to maintain nutrient balance. A well-maintained nutrient solution is key to thriving microgreens.

Avoiding Common Nutrient Problems

Nutrient imbalances can lead to problems like nutrient burn or deficiency. Stay vigilant and learn to identify signs of issues early. Addressing common nutrient problems early on will help your microgreens stay healthy.

Light and Light Cycles

In the world of hydroponic microgreens, lighting plays a starring role in the success of your crop. Providing the right type of light, choosing suitable grow lights, and maintaining consistent light cycles are key to your growing success. 

Adequate lighting ensures that your microgreens can carry out photosynthesis effectively, resulting in healthy and vibrant growth. Opt for natural sunlight if possible. 

If you don’t get enough natural sunlight, opting for fluorescent or LED lights, is the next best thing. This will help tailor your lighting setup to mimic natural conditions. Still leads to wonderful results. 

Choosing the Right Grow Lights

Selecting the right grow lights for your microgreens is an important consideration. Whether you’re using fluorescent or LED lights, understand their spectrum and efficiency to ensure your microgreens receive the light they need.

Light Cycles for Microgreens

Microgreens have specific light cycle requirements. Find out how long your microgreens should be exposed to light each day and maintain consistent light cycles to avoid issues like leggy growth. 

You can find instructions on the back of your microgreens seed packaging. 

Care and Maintenance of Your Hydroponic Microgreens

Once your microgreens are growing, it’s important to provide them with the care they’ll need in order to thrive. This will ensure your microgreens stay healthy and vibrant throughout their growth cycle.

Regular Inspections

Regular inspections are the foundation of successful microgreen care. Take a few minutes each day to examine your trays or growing system. 

Look for any of the following signs of issues:

  • wilting
  • discoloration
  • pests

Catching problems early can prevent them from escalating and harming your entire crop.

Pest and Disease Management 

Pests and diseases can be challenging to deal with in hydroponic systems so proper management is essential. If you notice any pests, like aphids or fungus gnats, take action immediately. 

Consider using organic pest control methods or beneficial insects to keep infestations in check. Additionally, maintaining a clean and sanitized environment can help prevent many disease problems.

Pruning and Thinning 

Pruning and thinning are necessary to ensure your microgreens grow well. As they grow, some microgreens may become crowded or develop leggy growth. 

Use scissors or shears to trim away excess growth and thin out densely sown areas. This allows adequate airflow and prevents overcrowding while promoting healthier growth.

Adjusting pH and EC Levels 

Monitoring and adjusting the pH and electrical conductivity (EC) levels of your nutrient solution is critical. Deviations from the ideal range can lead to nutrient imbalances and stunted growth. 

Regularly check and maintain the pH within the recommended range (usually around 6 to 7) and adjust accordingly. You can refer to the guidelines provided by your nutrient solution manufacturer.

Harvesting Microgreens: A Guide to Timing, Techniques, and Storage

Harvesting your hydroponic microgreens is truly rewarding after patiently (or impatiently!) awaiting their growth. This is the stage when you get to enjoy the vibrant flavors and nutrients of your own homegrown greens. 

Optimal Harvest Time

Timing is crucial when it comes to harvesting microgreens. The ideal harvest time varies depending on the microgreen variety but typically falls between 7 to 21 days after sowing. 

You’ll want to harvest when the first true leaves have developed, and the greens are at their peak flavor and nutritional value. Be patient and observe your microgreens closely to identify the perfect moment for harvest.

Harvesting Techniques

To ensure a successful harvest, follow these techniques:

  • Use clean, sharp scissors or shears to cut the microgreens just above the soil or growing medium. Avoid pulling them out by the roots, as this can disrupt the roots of neighboring plants.
  • Harvest your microgreens when they are dry to prevent clumping and easier handling.
  • Trim the microgreens to the desired length, typically around 1-2 inches above the growing medium.
  • Handle your microgreens delicately to avoid damaging the tender leaves.

Cleaning and Storing Microgreens

After harvesting, it’s essential to clean and store your microgreens properly:

  • Gently rinse your harvested microgreens under cool running water to remove any residual growing medium or debris.
  • Allow the microgreens to drain in a colander or on paper towels. Pat them dry if necessary.
  • Store your microgreens in a clean, airtight container with a paper towel to absorb excess moisture. This will help maintain freshness and prevent wilting.
  • Keep your microgreens in the refrigerator at temperatures between 32°F to 40°F (0°C to 4°C). They can typically stay fresh for about a week.

Remember that microgreens are best when consumed fresh, so aim to harvest only what you need to avoid waste. As you continue to grow and harvest microgreens, you’ll become more adept at identifying the optimal harvest time. As well as perfecting your techniques. 

Watch the video for the best Avocado Toast recipe to make with your newly harvested microgreens!

Troubleshooting Common Issues: Tips for Healthy Hydroponic Microgreens

While Hydroponic microgreens offer numerous advantages, you may still face some growing challenges. Below are some of the most common issues you might experience and how you can address them.

Yellowing Leaves

Yellowing leaves in your hydroponic microgreens can be a sign of nutrient deficiencies, overwatering, or improper lighting. 

To address this problem, first check your nutrient solution’s pH and EC levels to ensure they’re within the recommended range. Adjust as needed. 

Next, overwatering can lead to root suffocation, so make sure your growing medium has proper drainage. 

Lastly, ensure your microgreens are receiving adequate and appropriate light. Correcting these factors should help your microgreens regain their vibrant green color.

Mold and Mildew

Mold and mildew can be a headache for hydroponic microgreens, particularly in high humidity conditions. So taking precautions for prevention is the key. 

A few things to consider:

  • Improve air circulation by using fans
  • Reduce humidity levels
  • Avoid overcrowding your trays

If you spot mold or mildew, carefully remove affected plants, increase ventilation, and consider an organic fungicide if the problem persists. Be sure to maintain a clean growing environment to prevent future outbreaks.

Leggy Growth

Leggy growth is when your microgreens start to dwindle, weaken, and flop over. It’s a result of a lack of sunlight or sufficient lighting. 

To tackle this issue, move your trays closer to the window where they can get direct sunlight. If this isn’t an option, simply adjust your grow lights to be closer to your microgreens (within 2-4 inches).  This will ensure they receive enough light hours each day. 

Adequate light intensity and duration will help your microgreens grow more vibrant and strong. 

Picture of Sandra Campillo

Sandra Campillo

Sandra Campillo is an eco, vegan lifestyle and travel blogger and entrepreneur. Join Sandra and her community of readers on to learn how to live a healthier, more sustainable, and compassionate way of life.

Sandra's Story
Sandra Campillo
Shopping cart