The 3 Reasons Cloners Fail

Being the founder of PermaClone has allowed me to tour and keep in touch with a lot of hydroponic cloners, big and small! Through those relationships it has become clear that failure generally happens for 1 of 3 reasons.

Real quick! ...before I tell you the real issues, let's knock some variables that make for great refinements of cloning but don't make-or-break you. Throw out your concerns about water temps, pH, nutrients, hormones, lighting, humidity, vapor pressure deficit, the list goes on! NONE. OF. THESE. PREDICT. FAILURE. These variables are the refinements that produce better quality results or faster clones, but not the analog result--success or failure.


Ask anyone with cloner problems how their first run with the cloner was? 99% will say the first round was great! ….but as they added cloning cycles, the results diminished. Now this isn’t the case for everyone. When I created PermaClone I lived in Austin, TX and a hydro store in Dallas was far less familiar with this issue. You will discover why later in this article (this pertains to one of the 3 reasons).

So, generally, 99% of failed cloner stories start with a functioning cloner that slowly leads to failure after each cycle. Then that sad decision to shelf their system for good (..or sell it on Craigslist) with an emboldened determination that rockwool or plugs are the way to go. I knew one commercial grower in Colorado who literally threw away cloners when they reached complete failure rates. One of his theories was a plasticizer in the cloners. I had to respect that conclusion because he was of an era of growers exposed to vinyl tubing that caused failure because of a plant killing chemical in the plastic. I did (graciously) prove this grower wrong, and he upgraded to PermaClone and sterile techniques immediately.

But if Acom’s Razor is to be followed, then a cloner succeeding round one and slowly failing over time does allows for one primary (at least starting) hypothesis: sterility? For me that was an obvious and strong hypothosis. But eliminating all the sources was challenging and sterility involves attention to several variables. I wont go into them here. You’ll have to read my article on How to Sterilize Your Cloner...AND KNOW IT! and How to Sterilize PermaClone Collars with Confidence! For the details.

#2 Water Quality

Once you’ve established solid system sterilization--it is time for proper, regular water treatment. Remember my mention of the Dallas hydro store not being as worried about cloner failure? Well, in 2014 I was visiting a Dallas suburb with my close friend Kyi and (being the nerd I am) had chlorine test strips and a pH/TDS meter. As a grower I am always interested in a city’s water quality. For this Dallas suburb, GUESS WHAT? Chlorine levels out of the tap were a SOLID 4 ppm free chlorine. That is 1 ppm ABOVE pool strengths. Immediately I understood why that Dallas hydrostore was less wary of cloning failure. In retrospect this was obvious, but I simply hadn’t teased through all the variables. By that time I had managed six different grows, four on municipal water (treated) and two rural water wells and the hindsight was EUREKA! The rural grows were the most problematic! ...lots of cycle timing, concerns about temps, brown stems, tedious redundant sterilizations with hit-or-miss results.

The Dallas eureka moment was paramount because my 7th grow was (again) on rural well water and I could now deploy this new piece to the puzzle. Collars Sterilized (Check!), Cloner Sterilized (Check!) ...but water treatment? The new frontier! I had two 60 site EZ-Clones by that point and the experiment was clear as day. Chlorine spiked vs untreated. Untreated FAILED with this well water offering the worst results--the horrid slime in the cloner! At that time Clear Rez was available but not UC Roots or Watermax. I simply used 0.2 mL/gal bleach (4 drops/gal; 1 drop/liter) and chlorine test strips from local pool supply stores to ensure treatment levels were 3 - 5 ppm free chlorine.

Take home message: for predictable results, treat your water after system fill. With experimentation I learned a second spike AFTER cuttings are in place, but before additive is key! This surface sterilizes your cuts and any surfaces you touched while setting up and inserting clones.

There are several great product dedicated to water treatment in Hydroponics such as UC Roots, Watermaxx, Clear Rez, or 29% Peroxide. I still work with 0.2 mL/gal Bleach® (4 drops/gal; 1 drop per liter) and check the results with chlorine test strips from my local pool supply. The same can be done with these other products, but an ORP meter may be needed depending on the chemistry. 

For a detailed discussion on water quality and treatment read my article Hydoponics Water Quality and Water Treatment--A MUST READ!


I HAVE SOME GREAT NEWS! I have relied on water pumps for years to automate my grows and pump malfunction has been extremely rare! The single time I can think of, I recovered from. The bad news is there’s another form of pump failure and it’s not due to the’s called “I didn’t plug in the pump” failure--let’s call it Pumps Unplugged. Luckily I’m all about counteracting my deficits to attention and found the solution--CYCLE TIMERS!

Cycle timers end that Unplugged Tour for good. Here how it goes. Your pump is ALWAYS plugged in. PERIOD. Your cycle timer is set to long “on times” and  5 - 30 min “off times” (depending desired temperature--we recommend 75 - 85--no more, no less). When you want to inspect the cloner? Spin the Cycle Timer “on time” to it's minimum time in seconds, the pump shuts off and you IMMEDIATELY dial it back to the desired "on time", while your off time is initiated (5 - 30 min off). You now have 5 - 30 min to check on that status of your clones.  This tiny little adjustment has 100% eliminated the most common form of pump failure--Pumps Unplugged.

For good measure, I must address another cause of pump failure. The clogged pump. It can happen at the intake or misters. Do not let clones grow past your manifold and certainly avoid vegging clones in a high-through-put cloning situation. When clones achieve prolific roots in the 1 - 4 inches (2.5 - 10 cm) range, move to your next stage of growing is a good rule of thumb. Vegging them is fun (and makes for great shots on social media) but it is not good practice! Luckily vegging in the cloner is less likely a cause of immediate failure and more likely to cause small root dabris to build up over time, causing a failure down the line and unpredictably. PermaClone is about predictable results!


  • When I put my clones in the ez clones should the stems be in the water or are the misters enough.

  • Hi Ace,

    If your cloner doesn’t get above about 87 °F (31°C)—and your system is sterile by our techniques—you don’t need cycle timing.

    Cycle timing is for pump overheating your water beyond 87 °F (31 °C) OR, for many people (unknowingly) if you need to run colder temperature because you system is NOT sterile yet.

    (I also use cycle timers to set off cycles when checking cuttings…prior to keep a cycle timer, once-in-a-while I would forget to plug the system back in and kill cuttings. With a cycle timer, I dial on a short off time to check on the cuttings without unplugging. If I forget to dial the system back to a short off time, no problem…because worst case scenario I left only 30 min off times…I haven’t left a cloner unplugged since!:) …but this is off topic.

    If you want to get your temperatures down, you can cycle time based on percent reduction ON time. For example, 30 min off / 30 min on = 50% reduction in pump heat output. Another example, 5 min on / 30 min off (85% reduction in pump on-time).

    Keep in mind: measure temperature from the outside of the system with an IR thermometer. Once your system is set, don’t insert thermometers or other meters for risk of contamination. Treat cloning like tissue culture. Don’t touch the insides of your cloner.

    Please email me any time with questions, comments or concerns.
  • HI “grower” …I’m super happy I could help. As I mentioned, I went through the same rough times and the few changes I painstakingly discovered and share have made cloning easy, predictable, and highly automated for myself and our customers.

    I hope you’ve read our other articles discussing techniques and additives that yield profound results.

  • Thank you so much for this article, was at a total loss until reading it. Being disabled, I grow a lot of small plants, so need a lot of clones.
    Just like you discribed, the clones in my aeroponic cloners started failing over time, and this spring-summer most of the cuttings died. There was a lot of slug goo like stuff on the stems.

    Turns out that it was more my water then anything else. In the winter I use rain water, and switch to the river when the rain stops, thus the almost total clone failure in the summer.
    Bit frustrating for sure. I cleaned between batches with bleach, but used my live water after words. My water does run through a large sand rock type setup, but not chlorinated.
    My stepson borrowed one of my cloners, and had no problems. He used city water of course. I’m now using distilled water with bleach. Thankyou for putting me on the right path.

    PS A very experienced guy was coming over the day I read your article to help me figure it out. We never would have figured it out, because he uses well water, and has no problem. Must be a deep well.

  • What should I set my timer to? How long should the sprayers be On?how long should the sprayers be off?
    What temperature should the water be at? 75-85?


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