The Most Common Problems With Germination of Cannabis Seeds

Our hope is that we can help you detect, and even prevent, some of the most common problems that can occur when germinating your seeds. Know that problems with germination can often appear not because of the quality of seeds, but because of mistakes somewhere in the setup or with the steps in the germination process. If you know the cause why the germination of your seeds has failed, this guide can help you prevent this from happening again.

Don’t think that poor germination is always your “fault”. There can be many factors that can make germination difficult or impossible. To ensure that your seedlings start their life off on the right foot, it is important that the environment is optimal. The temperature, humidity and soil quality are all variables that are important to control. The pH in the water is also an important variable. These can be situations where poor germination is pretty much inevitable. Sometimes even things like a broken or incorrectly calibrated EC meter than lead to poor germination results.


Many cannabis growers are still pre-germinating seeds in a glass of water or with the “paper towel method”. In the first case they would pre-soak the seeds in water for some hours or even days and in the second they put seeds between wet paper towel sheets and have them germinate there.

Pre-soak The Seeds In Water

The drawback with these pre-germination methods is that they are very error-prone. The potential problems from these methods like fungus growth or damage to the sensitive tap roots when moving the seed to a new medium are normally outweighing their supposed benefits. Good quality seeds don’t normally require pre-soaking, whether it’s in water or with wet paper towels so that it is recommended that you don’t use these methods. Have your seeds germinate in their final pot, which helps keep your risk down for a higher chance of germination success.


If your seeds won’t germinate, the first thing that you should do to find the cause is to look at the seeds. Seeds that won’t germinate can have changed their color, most of the time they may have gotten noticeably darker. There can also be a white coating at the rounded end of the seed. When you crack open the seed you can sometimes notice that the embryo has become soft.

The other possibility is that seeds started out alright at first, the seeds cracked open and the tap root appeared but growth stopped.

A common cause for failed germination is when the substrate became too dry at some point. You can check whether this was the case when you crack open the seeds. An indication that the seed needed more water is if the embryo looks healthy, white and firm. If you tried to germinate outside, you should also consider whether frost may possibly have stopped germination.


If you spot a white, fluffy looking substance on one end of a seed that turned dark it is very likely fungus, one of the most common reasons for failed germination. Fungus can appear under wet and cold conditions and in an environment where oxygen is lacking.

There can be many reasons for a fungal infection like poor soil quality, incorrect pH, overwatering, high humidity, poor air circulation or cold temperatures.

When you open a seed that has been infected by fungus, the seed will have rotted and has turned into a soft, yellowish liquid.

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GROW TIP: Promote air circulation when using mini greenhouses. However, a completely closed mini greenhouse only makes sense if you want to root clones and cuttings. Seeds and young seedlings need good air circulation and a well-aerated growing medium. The only thing that needs to be kept moist is the soil or growing medium. Ambient air humidity is best kept at 50%-80%. If you want to cover up the seed tray for whatever reason, then make sure that the lid is at least half-open for adequate air circulation and humidity levels.


In those cases where the seed started out normal and developed a tap root, but then stopped growing, fungus can also be a reason for this. But it is also possible that the seed was killed by high temperatures, such as when you used a heat mat and you set it at a too high temperature.


One other reason why an emerging seedling could have been killed prematurely could be if the EC is too high. If you suspect the EC, you should check your substrate’s EC. While you are at it, it is always a good idea to check your EC meter and calibrate it if neccessary.


Tap water with its often high levels of chlorine, fluoride and salts can be another reason for a failed germination. The minerals and salts can stunt the growth of the very sensitive seedling. If you really need to use tap water, fill a bucket with hot water and have it sit outside for a day so the chlorine can evaporate. Even better, use bottled water for germination.

Either way, the correct pH for your water is very important. If you germinate in soil, you may have to adjust the water pH to 6.5 and if you germinate in rockwool even lower, to about 5.6-5.8 pH.

GROW TIP: When you water your substrate for germination, use pure pH adjusted water only. Don’t give any nutrients or teas. Seeds or young seedlings won’t require them and giving pure water is the best for promoting healthy root growth.

GROW TIP: Avoid jiffys and peat pellets. In contrast to what advertisements may say, Jiffys and peat pellets are not optimal for seed germination. Many times, those have an alkaline pH that would hinder germination rather than help it. If you have poor results with a particular product, don’t use it next time and switch to another germination method.

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