The roots were brown. Not light tan, not slightly off-white, brown and slimy, sitting in water that smelled like a neglected fish tank. That was my AeroGarden Harvest buy on Amazon about six weeks into my first basil grow, and I genuinely thought I’d broken the whole thing.
I hadn’t. But I also didn’t know what I was looking at or how to fix it, and the AeroGarden support page wasn’t exactly a diagnostic flowchart. So I’m writing the guide I wish I’d had. If your plants are dying, yellowing, burning at the tips, or just sitting there not doing anything, one of the five problems below is almost certainly why.
Quick-reference table first, then the full breakdown:
| Symptom | Likely cause | First thing to do |
|---|---|---|
| Brown, slimy roots; bad smell | Root rot | Water change + hydrogen peroxide rinse |
| Yellow leaves, slow growth | Nutrient deficiency or overdose | Check dose, adjust nutrients |
| Brown leaf tips, bleached patches | Light burn | Raise the light arm |
| Green water, algae on pods | Light getting into reservoir | Cover unused pods, wrap reservoir |
| Wilting, no growth, warm water | Pump failure or stagnant water | Clean the pump, check water level |
Root Rot (Brown, Slimy Roots)
This is the one that looks the worst and panics people the most. Healthy roots are white or very pale cream. If yours are brown, soft, and slimy, and the water smells like anything other than slightly earthy, you’ve got root rot.
Root rot in hydroponics comes from a few places: water that’s too warm, not enough oxygen getting to the roots, or a pathogen called Pythium that loves stagnant, warm conditions. The Harvest’s reservoir is pretty small, which means temperatures climb faster than you’d expect, especially if you’ve got it sitting on a counter near an appliance or in a sunny spot.
Here’s how to fix it:
Drain the whole reservoir. While it’s empty, take the roots out and rinse them under cool running water. Then mix up a hydrogen peroxide solution, about 3ml of standard 3% hydrogen peroxide per liter of clean water, and soak the roots in that for about five minutes. It’s going to look alarming. Some of the dead root material will come off, which is fine. What you want to keep is anything still white and firm underneath all the brown.
Scrub the reservoir with that same hydrogen peroxide solution before you refill. Rinse it well, then add fresh water and nutrients at the correct dose. Keep the water level a bit lower than max so the roots get some air exposure at the top.
One thing that actually helped me: I moved the Harvest off the counter near the fridge. I think the motor heat from the fridge was warming the whole counter surface. Sometime after I moved it, the root situation stabilized. I can’t say for certain that was the cause, but the timing lined up.
Nutrient Problems (Yellow Leaves, Stunted Growth)
Yellowing leaves have about four different causes in hydroponics, but in an AeroGarden specifically, the most common one is a nutrient dose problem. Either too little, or, and this one surprises people, too much.
The AeroGarden app and the machine itself remind you to add nutrients every two weeks. What they don’t always make clear is that the dose on the bottle is calibrated for a full reservoir with actively growing plants. Early on, when the plants are small and the roots aren’t taking up much, I’d sometimes get nutrient burn from dosing at full strength. The leaves would yellow at the tips and then curl slightly.
The Miracle-Gro AeroGarden Liquid Plant Fertilizer buy on Amazon is the obvious choice if you want something matched to the system. It’s convenient, it works, and you don’t have to think about ratios. My actual complaint is the bottle size, the 3 fl oz version runs out faster than you’d expect if you’re doing regular top-offs with nutrients, and the per-ounce cost is genuinely annoying compared to third-party options.
If you want to stretch your budget further, the liquid fertilizer from the IDOO-compatible line buy on Amazon works in the Harvest and costs noticeably less per dose. I’ve run it through two herb grows now without any issue. The concentration is a bit different from the AeroGarden formula, so start at half the recommended dose and scale up, yellowing that doesn’t resolve after a week usually means you need a bit more; yellowing that gets worse after adding nutrients usually means back off.
There’s also an A&B two-part formula buy on Amazon that’s worth mentioning if you want more control. It’s set up so you mix Part A and Part B separately into water rather than using a single pre-mixed liquid, which lets you dial in ratios as your plants mature. At around $11 for a pretty substantial supply, the value is there. The directions say 5ml of A and 5ml of B per liter of water, which I’d treat as a ceiling rather than a starting point for seedlings.
For a more detailed look at how these options compare, I wrote up a full AeroGarden nutrient alternatives breakdown that goes into the third-party stuff in more depth.
One actual deficiency worth knowing: if the yellowing starts on the older, lower leaves and works upward, that’s usually nitrogen. If it starts on new growth and the veins stay green, that’s more likely an iron or manganese issue, which is often a pH problem rather than a missing nutrient. The Harvest doesn’t have a pH display, so grab a cheap pH pen if you’re troubleshooting this one.
Light Burn (Brown Leaf Tips, Bleached Patches)
This one took me a while to accept because I kept thinking, how can a grow light that’s designed for this system be too strong for the plants in it?
But it can. Fast-growing plants like basil and mint will eventually get close enough to the light that the canopy starts burning. You’ll see it as browning on the very tips of leaves first, then pale bleached patches on the top surfaces. It looks different from nutrient burn, nutrient burn tends to affect edges and tips uniformly, while light burn is usually concentrated on whatever’s closest to the bulb.
Fix: raise the light arm. The Harvest’s arm adjusts in stages, so go up a level and see if new growth looks healthier over the next week. Also check your timer. The default AeroGarden setting is 16 hours of light for herbs, which is fine for most things, but if you’ve got the light very close and you’re growing something sensitive, dropping to 14 hours can reduce stress without meaningfully slowing growth.
Lettuce is especially prone to this, I’ve got a longer piece on managing light for lettuce at [/posts/how-to-grow-lettuce-in-an-aerogarden-without-tip-burn/] if that’s what you’re growing.
Algae and Green Water
The reservoir turns green. The water looks murky. Sometimes there’s a film on the surface or green growth around the pod holes.
This is algae, and it grows when light gets into the water. Algae won’t necessarily kill your plants immediately, but it competes for nutrients, can gum up the pump, and once it’s established it’s annoying to get rid of.
The fix is blocking light from the reservoir. Cover any empty pod holes with the little plastic caps that came with the unit, if you’ve lost them (I lose them constantly), black electrical tape works. If algae is already in the water, do a full water change, scrub the reservoir walls with a diluted hydrogen peroxide solution, and then cover those gaps before you refill.
Some people wrap the outside of the reservoir in dark material. Honestly I’ve never bothered, but if you’re dealing with recurring algae and the unit is in direct sunlight, it’s worth trying.
Pump Failure or Stagnant Water
Nope, this one isn’t obvious until you actually listen for it.
The pump in the Harvest is small and fairly quiet, which means it can stop working or get partially blocked without you immediately noticing. But stagnant water means no oxygenation, and roots sitting in warm, still water will develop rot within a few days.
Press your ear near the base of the unit and listen. You should hear a low hum and some water movement. If it’s silent, or if the water isn’t circulating (you can usually see some movement if you look at the surface), the pump needs attention.
First thing: check the water level. The pump needs to be submerged to work, and if you’ve let the level drop too low, it’ll run dry and sometimes stall. Refill to the correct level and see if it restarts.
If the level is fine, the pump may be clogged with mineral deposits or root material. Unplug the unit, remove the pump, and soak it in a 50/50 white vinegar and water solution for an hour or so. Rinse well and reinstall. This fixes it probably 70% of the time in my experience.
If it’s genuinely dead, AeroGarden sells replacement pumps and they’re not expensive. Don’t just leave it and hope, stagnant water will kill everything in the reservoir within a week.
Most AeroGarden failures come back to one of these five things, and most of them are fixable without buying anything new. The one I’d tell you to watch most carefully is root health, just because it’s the one that moves fast and looks the most alarming. Check your roots every time you add water. White and firm is what you want. Everything else flows from there.