Hydroponics 101: The Missing Manual

I recently had a conversation with someone who assumed hydroponic gardening was a bit more tedious than traditional growing. It isn’t, but there is one teensy problem for folks just starting out — the instructions that ship with boxed gardens and those beginner DIY videos are really meant to get 90% of new growers from point A to point B as quickly as possible with the assumption that conditions are perfect, nothing will go wrong and covering the bare minimum of details is good enough.

Here’s what they don’t tell you…

1. Germinating seeds do not need nutrients.

A seed comes equipped with everything it needs to germinate and sprout. If you’re providing light and adding nutrients, all you’re doing is creating an optimal environment for algae growth. Don’t do it. Plan to start adding nutrients after the cotyledons (seed leaves) are well developed and the first set of true leaves start to emerge.

2. Cotyledons (seed leaves) turn brown and fall off.

One day you get all excited because your seedling has two sets of leaves and a few days later you start to panic because it looks like it’s dying. It’s perfectly normal for that first set of leaves — the seed leaves — to turn brown and fall off. Once your seedling has started to develop, they’re no longer needed.

3. Different seeds need different germination methods.

Some seeds can be tossed into a bit of growing media and they’ll germinate like gangbusters. Others aren’t quite as cooperative. Some seeds — like cilantro — are easier to germinate if you crack them first. Others — like peony poppies — need to be cold-stratified. Some like a cool environment, some like it warm and some will germinate better in a Ziploc bag on a damp paper towel. Some need light and others want darkness.

Before you try to grow something unfamiliar, make sure you know what that particular seed prefers. Check to see if your local extension service has a web site with a searchable database. Check the images of seed packets on one of the many retail web sites. Worst case, search for seed germination resources or “how to germinate <insert-name-of-plant-here>”.

Use a reliable seed source. Johnny’s Selected Seeds and Baker Creek Heirloom Seed Company are two favorites among hydroponic growers. I’ve also had good luck with Seed Needs.

4. You can plant more than one seed per basket.

“If you only plant one, it won’t germinate. If you plant three, they will all germinate.”

The general rule is one large seed, 2-3 medium seeds or 3-4 tiny seeds per basket. Whether you thin them after germination really depends on the plant. You can easily leave several chives in the same basket, but lettuce, vegetables and flowers will do better alone. A couple of thyme plants can coexist, but a few fast growing mints will eventually suffocate each other. Use tweezers to move the smallest, least healthy seedlings to another basket.

5. Don’t overcrowd your system.

Just because that Aerogarden has 9 holes doesn’t mean you should use all of them. For fruiting plants like tomatoes and peppers, you’ll use 1 of every 3. For herbs and lettuce, you can use every hole, but only if you’re doing frequent harvesting — every 3 days or so.

Know your plant’s growth habit. Petunias grow beautifully in an Aerogarden, but one well-established petunia can cover the entire surface of your 9 hole garden. Grow petunias in a smaller garden and save the 9 holes for more vertical plants.

Plan ahead. If you think you’re going to need to move a plant from a multi-hole garden to a Kratky jar or bucket, do it before the roots are too big to safely remove the plant from the grow deck.

6. Don’t drown your air roots.

Hydroponic plants feed through the root system that is submerged in nutrient solution. The roots are also pulling a small amount of oxygen from the water but it’s not enough — even if you’re aerating the water with a pump or air stones.

This is where air roots take up the slack. They’re completely exposed above the water line where they take advantage of free oxygen.

A good rule of thumb is to keep the bottom 1/2″ of your growing media submerged until your roots reach the bottom of the media. Then keep the bottom 1/8-1/4″ of media submerged. Once you have lovely white roots growing out the sides of your media and a sizable mass hanging down, the media doesn’t have to be submerged at all. I try to keep the bottom third to one-half of my roots in water.

7. Algae happens. H2O2 (hydrogen peroxide) is your best friend.

Try to avoid algae by keeping light away from your nutrient solution and growing media. If you’re doing the Kratky method in Mason jars, you can use amber jars, paint your jars a dark color or invest in 3D-printed sleeves to block the light. If you’re doing larger containers, black storage bins work well.

Add 2-3 teaspoons of 3% H2O2 to every gallon of water. Cover the tops of your baskets and net cups with aluminum foil or dark tape to keep the light away from your growing medium. The covers can be removed when plants have developed enough foliage to provide natural shade.

Don’t forget to cover the empty unplanted holes. Some systems have custom covers available but innovative growers have come up with all sorts of solutions from dark tape to ping pong balls, corks and decorative figurines.

When you do develop an algae problem on your growing media — and you will — a quick squirt of 3% H2O2 will usually take care of it. It’s easiest to apply if you keep it in a tattoo wash bottle, but a saturated q-tip will work too. When treating for algae, check the water and containers to make sure they’re still clear. Do a deep clean and water change if necessary.

Don’t forget to check  your roots. Rinse them in cold water and rub gently to remove anything that’s green. If your roots are slimy, try to remove all the slimy bits. You might have to flush the roots in plain water for a few days to get them healthy.

8. Keep your garden clean.

Inspect your containers weekly. Wash with hot soapy water to remove dirt and algae. Scrub with white vinegar to remove mineral deposits. Do a complete nutrient solution change once a month. If there’s no algae, pour the spent solution in your outdoor garden. Remove dead organic matter from your baskets, net cups, and growing media.

9. Buy 12% or 35% H2O2 and make 1% or 3% when you need it.

You’ll need various solution strengths for different purposes. No need to keep all of them on hand because a stronger solution can always be diluted to make a weaker one:

( current strength / target strength ) – 1 = amount of water to add

Suppose I have 99% isopropyl alcohol and I need 70%:

(99 / 70) – 1 = 1.41 – 1 = .41

I need to add .41 parts water to 1 parts 99% IPA to make 70% IPA, i.e, round up and add 1/2 cup water to 1 cup 99% IPA,  1/2 quart to 1 quart, 1/2 gallon to 1 gallon, etc.

If you don’t have a calculator handy, you can use my solution strength converter spreadsheet. Make a copy and plug in your own values.

10. Pests happen.

Aphids, fungus gnats, and spider mites are the most common. It’s important to act quickly before you end up with a full-blown infestation.

General Insecticide Recipe

1/4 c. Dr. Woods Peppermint Liquid Castile Soap
1/4 c. Dr. Woods Tea Tree Liquid Castile Soap
1 c. 70% Isopropyl Alcohol
1 tbsp. 1% Hydrogen Peroxide
Room temperature water to make 2 quarts (1/2 gallon)

Dilute your H2O2 to 1% before measuring. Mix all ingredients in a 1/2 gallon garden sprayer. Set the sprayer to dispense a fine mist. Spray all foliage, stems and flowers. Make sure you spray both tops and bottoms of all leaves.

Fungus Gnat Remedy

If you see fungus gnats, there’s a 99.9% chance you have both adults and larvae and you’ll need to tackle both at the same time. Use sticky traps or a Katchy Indoor Insect Trap (or both) to deal with the adults. You may need to use multiple traps if your plants are spread across a larger area.

To treat the larvae, saturate your growing media every 2-3 days for 2 weeks with mosquito bit tea.

Mosquito Bit Tea Recipe

4 tbsp. Mosquito Bits
1 gal. hot tap water (not boiling)

Mix all ingredients in a 2 gallon container. Let the solution steep for 30 minutes. Add 1 gallon of cold water and let the solution cool completely before using it to water your plants.

The soggy bits can be messy, unattractive and clog the spout of your watering can. You can contain the bits in a nut milk bag, spice ball, or a DIY packet made with paper coffee filters and staples (or water-resistant tape).

11. Young herbs need pruning too.

Learn how to prune, do it early and often. To prune most of the bushy herbs — basil, marjoram, mint — pinch off the tips down to the 2nd or 3rd set of leaves. As they grow bigger, harvest the top 1/3 to 1/2 of the longer stems, pinching just above a set of leaves.

Maintain the shape of your parsley, cilantro, and dill by clipping the outside stems. These herbs will continue producing from the center.

Bonus tip: dill is a drama queen. One day it’s standing tall and proud. The next day, it’s weeping like it was doused with onion juice. You can give it a trim, tie it to a trellis or ignore it. It’s fine and it will recover.

12. Harvesting lettuce: pinch or haircut?

Either. Or both. It depends.

The sturdier varieties with bigger leaves — Paris Island Cos, Black Seeded Simpson — will do well when you pinch the larger outer leaves giving the inner leaves more room to grow.

The more delicate varieties — the heirloom mixes — can also be pinched, but cutting straight across with a sharp pair of snips to remove the top 1/2 to 2/3 is a bit easier to manage. Over time, the outer remnants may shrivel and brown. Use a pair of tweezers to pluck them off and keep the plant looking nice and tidy.

13. Topping off: plain water or nutrient solution?

It depends on a few things: how thirsty your plants are and how fast your water evaporates. Imagine you’ve just refreshed your kratky jar growing cherry tomatoes with 5 gallons of nutrient solution that’s 98% water. Tomatoes are seriously thirsty — especially when they’re producing fruit. I.e., they’re consuming water faster than they’re consuming nutrients and the nutrient concentration is increasing. If you’re constantly topping off with quarts of nutrient solution, you risk burning your tomato plant’s roots as the solution in your kratky jar gets stronger and stronger.

A general rule of thumb is to top off with plain water until you’ve replaced at least half of the original volume. If you’re getting close to a cleaning / water change, continue topping off with plain water and refresh the solution when you change the water. Otherwise, top off with nutrient solution. Do not top off with nutrient solution more than once or twice between water changes.

14. You can store what you harvest.

You have to prune and harvest to keep your plants healthy, but now you have to figure out what to do with it.

Lettuce will keep for several days in produce bags or the OXO Good Grips GreenSaver Produce Keeper.

The OXO Good Grips GreenSaver Herb Keeper works well for herbs, but you can also freeze them. Add chopped herbs to a silicon ice cube mold, fill with water or olive oil and freeze. Transfer the frozen cubes to a labelled freezer bag. If you’ll be using them in the next day or two, sandwich them between two damp paper towels and store inside partially sealed Ziploc in the refrigerator.

15. You can move hydroponic plants to soil and outdoor gardens.

Hydroponic plants that have been growing indoors aren’t used to soil or harsher outdoor conditions — hotter, brighter sun, stiff breezes and heavy rain. You can transition to both soil and outdoors, but don’t do both at the same time.

To transition to soil, carefully remove the growing media from the basket. Use scissors to cut away the basket if necessary. This would be a good time to do one final trim on the roots. Keep the plant in its growing media and set in a shallow bowl of cool water while you prepare the pot.

Add a high quality potting mix to an appropriately sized container. Do not pack the soil. Water thoroughly and let the excess drain. Use a dibbler to make a hole the same diameter and depth of your basket. Move the plant to your prepared hole using the dibbler to position the roots. Add more soil as necessary and pack just enough to hold the plant in place. Spray the top of the soil with water to make sure everything is very damp. You want the soil to be just this side of soupy. Water and monitor for 3-4 days, allowing the soil to dry out a little more each day.

To transition to outside, move the plants to a shady outdoor spot for 2-3 hours on a calm day. Gradually increase the amount of time and sunlight over the next 7 days. If your local weather forecast is calling for a 3 to 4 day stretch of overcast days, you can move the plants to a calm spot and leave them outside 24/7.

16. You can root seedlings in water and move them to a hydroponic system.

Make a slit down the side of your growing media and carefully run the seedling with its roots straight down the center. If the roots are long, just let them hang out the bottom. You can trim them back to about 1″ if they’re exceedingly long. Carefully thread the roots through the bottom of your basket or net cup and drop into your system.

Useful Tools

My favorite nutrients are distributed by General Hydroponics. For general feeding, I add 6ml of Flora Micro, 6ml of Flora Gro, and 6ml of Flora Bloom in that order to 1 gallon of water mixing well after each addition. If I’m feeding tomatoes or peppers, I also add 5ml of FoxFarm Bush Doctor Cal-Mag.

FoxFarm nutrients are a reasonable alternative to GP. Just make sure you source the hydroponic versions. They’re not the same as the soil versions.

I’ve used both Aerogarden sponges and TISOHUGO sponges to grow my own seed. Personally, I think the TISOHUGO’s are of better quality. Some people have complained about excessive algae growth on the Aerogarden sponges. YMMV.

I use Ulrempart Plant Spacers a.k.a hole covers to keep the light away from the empty unplanted holes in my standard Aerogarden grow decks. These spacers do not fit the seed starter grow decks, but there’s a quick easy 3D printable solution.

Disclaimer: All Amazon links in this post are affiliated. This means I may receive a small commission if you make a purchase.

Posted in gardening and tagged , , .


  1. # 15
    Hydroponic plants that have been growing indoors aren’t use to soil or harsher outdoor conditions

    Should that read ‘aren’t used to..’?

Leave a Reply

Your email address will not be published. Required fields are marked *