Hydroponics 2.0: What’s going wrong and how do you fix it?

published on 23 December 2025

Guest Contributor: Cassey Anderson, Horticulture Agent, Colorado State University Extension

Hydroponics make it convenient to grow indoors any time of the year, keeping your garden away from pests, and your harvest at your fingertips. In this article, Guest Contributor: Cassey Anderson, Horticulture Agent, Colorado State University Extension shares her tips for keeping your indoor garden healthy.

We explored the basics of hydroponic growing in our Hydroponics 101 article, so now let’s get into some details about what to do when something isn’t working quite right. This, of course, is not an exhaustive list but may help get you on the right track if you’ve been trying hydroponic growing in your own home.

Algae

Are you seeing green growth on your growing medium, or floating in your hydroponic solution? This is a very common issue that is thankfully very easy to solve. Algae grows when the right combination of light + nutrients + water are present. These are also the main components required for successful growth for your hydroponic system. Thankfully, there are options to combat algae growth!

Pretty for photos, but asking for trouble!
Pretty for photos, but asking for trouble!

First off – ensure that no light is reaching your nutrient solution, this may require painting containers, covering planting holes etc. You may notice that most systems don’t look like the picture here—the water area is not visible to light. If you already have algae growth, you can clean your system thoroughly and start fresh. Many growers also recommend using a 3% hydrogen peroxide treatment, but know that a little goes a long way, too much can kill plant roots. Overcrowding – it can be tempting to plant a few extra plants to ensure good growth – but this can lead to development of disease pressure, reduced rooting area. There are two main ways you can overcrowd a hydroponic system – the first, is too many plants in a net cup or cell. It can be tempting to leave all 15 lettuce seedlings that emerged, and if you’re harvesting microgreens or baby greens perhaps you can get away with it, but for mature plants, or larger plants like tomatoes or cucumbers it is very important to thin the plants down to 1-3 (depending on what you’re growing) to ensure the best conditions for your plant.

The second way that overcrowding can occur is through planting every single available cell. This is so easy to do when you’re working with newly planted seeds or transplanted seedlings as the available space looks endless. However, as plants grow they take up that space and you can develop competition, risk increased pest or disease pressure, or have issues with harvesting access. Better to plant sparingly with any new varieties and then plant more densely if you end up having more room than you thought!

Root Rot

Hydroponic roots should be white and firm. However sometimes you may find brown or slimy roots. If you do, it is likely you have root rot. It is important to quickly remove any affected roots, prune any dying leaves of the plant above. Often root rot occurs because there is a problem in your system – double check your pump, add a small amount of hydrogen peroxide (2 tsp of 3% solution per gallon). It could also be warranted to change out your water for new water with fresh nutrients and ensure you’re not adding too much for plant health.

Wrong plants

Some plants are wonderfully well suited to hydroponic growing, think lettuce, kale, chard, bok choi, peppers, determinate tomatoes. Others, not so much: root vegetables, onions, potatoes, squash or pole beans. Successful plants often do not require pollination, have fibrous roots rather than tap roots, or are successful with care and precision (manually pollinating peppers and tomatoes). Plants that are going to struggle more often will be those that grow in the soil, that need substantial support or space to grow. This is not to say they are impossible, but they are going to take a lot more care and planning and the end result may be mixed.

Pests

A big motivator of many new and experienced hydroponic growers is the lack of pests. However, because we often grow a lot of the same variety of plant once a pest issue starts it can explode rapidly. The best way to manage pests is to prevent getting them to begin with – so be cautious when bringing plants in from outside, or purchasing seedlings. To combat them you can use a variety of approaches. Sticky straps and soapy water sprays can both help. However, a benefit to the hydroponic system is that if you do have to admit defeat you can close it all down, remove all your plants, clean your system and start fresh.

Lack of regular cleaning/maintenance

Hydroponic systems can get a little gross even with good maintenance and care, so regularly closing the system down and cleaning every part (including your pump and tubing) is important for successful growing in the long term. Plus, since we’re adding nutrients (which are salts) into the system, they can build up in areas where air and water meet, so the more frequently you can clean those deposits the happier and healthier your plants will be!

Nutrients

If your plants aren’t growing, are looking poorly, or are developing spots, it could be that your nutrients are off. Be sure you’re using a water-soluble nutrient either liquid or powder that is designed for hydroponic systems. There are many good options. Additionally – be sure to mix your nutrients when you plan to add them, if you pre-mix you may cause some of the nutrients to precipitate (fall) out of the water solution and not be available. You can also use some tools to test your water nutrient levels. Some good tools to find are a pH monitor, a tool that measures EC or electrical conductivity, and one that measures TDS or total dissolved solids. These can be purchased as all-in-one units, but you’ll often get better quality tools by purchasing them separately. There is no one-size-fits-all number to aim for but having the right tools to measure where you’re at can certainly help!

I think that’s about it for now, as always reach out to your local Extension office if you have additional questions.

As always, reach out to your local Extension office for further information if you have any questions.

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