The Bio Dude | Your #1 shop for all things reptile! | Spend $150 get $8.95 Flat Rate Shipping | Current order processing time: 2-3 business days | NOTICE: We currently cannot ship live plants to California

Stagnation in Bioactive Setups: How it Happens & How to Prevent It

Stagnation in Bioactive Setups: How it Happens & How to Prevent It

Pee-yew, what is that SMELL? If you open the door to your bioactive enclosure and it smells foul instead of pleasant, then you might be dealing with a case of stagnation.

What is stagnation? Stagnation is an overgrowth of anaerobic (“bad”) bacteria caused by poor ventilation and/or poor drainage in a vivarium. Bacteria are ever-present in an environment, and perform many different roles: improving soil structure, recycling nutrients, increasing water retention, decomposing waste; assisting carbon, nitrogen, and water cycling; and even protecting plants and animals against disease — just to name a few. Most of the bacteria that perform these functions are aerobic (“good”) bacteria, which require an oxygenated environment.

Maintaining a diverse bacterial population in an ecosystem is essential to keeping it balanced and healthy. Anaerobic bacteria do perform some beneficial functions, like breaking down nitrates. However, when conditions change to throw bacterial populations out of balance, that’s when problems occur. The rank stench of hydrogen sulfide is just the tip of the iceberg; many anaerobes are pathogenic (which means that they make plants or animals sick), and once they start to get the upper hand, they’ll outcompete and even kill neighboring aerobes.

How does stagnation happen in a bioactive setup?

As the saying goes, “Too much of a good thing becomes a bad thing”.

Water is essential to a bioactive enclosure’s functionality. It plays a major role in keeping your plants thriving, your CUC populations stable, and maintaining comfortable humidity levels. However, when there’s too much of it, it overwhelms the drainage layer (if there is one) and crowds out the oxygen. This creates an anaerobic (oxygen-deficient) environment. Considering that most soil bacteria prefer a neutral pH with plenty of available oxygen when that oxygen isn’t available anymore, those beneficial bacteria die off and get replaced by enthusiastic anaerobic bacteria which thrive in that kind of environment.

Signs of stagnation in a bioactive enclosure are a foul odor, soggy soil, and wilting/dying plants.

How do you prevent stagnation in a bioactive setup?

First, you need well-draining soil. Materials like coconut fiber and peat moss tend to hold on to water aggressively, and soil with too much of these ingredients can get choked with water quickly. They’re not bad, but they need to be balanced out with larger particles and materials that don’t absorb water, like sand, gravel, bark pieces, and leaf litter. A thicker layer of substrate also helps protect against overwatering and stagnation. Periodically rake through the substrate with a fork to help prevent compaction, and use CUC that like to dig, such as giant canyon isopods, superworms, or earthworms.

If you’re setting up a tropical environment, then a drainage layer is a requirement. A drainage layer provides a place for all the water it takes to nurture tropical plants and humidity levels to go. However, a drainage layer isn’t a guarantee against stagnation. If it gets too full and doesn’t have a chance to drain out, then that stagnant water will start to breed bad bacteria. Keeping an eye on your drainage layer, avoiding overwatering by monitoring soil moisture levels, and having a way to drain excess water out of the drainage layer will all help prevent stagnation.

The more plants you have, the harder it will be to overwater because those plants will be taking water out of the soil and putting it into growth. This is especially the case if you have large plants, rather than lots of small ones, as large plants have equally large and thirsty root systems. Just take care not to over-plant!

Keeping the enclosure well-ventilated can also help remove moisture from the soil and prevent it from getting soggy. A computer or desktop fan does a good job of keeping the air moving. Using a heat lamp as your primary heat source can also help keep air circulating and remove water from the soil. However, note that these methods can make it harder to maintain consistent humidity levels, so you may find yourself misting the enclosure more often to compensate.


Can stagnation be fixed?

If the soil isn’t too far gone, draining your drainage layer may help by reintroducing oxygen and killing off the bad bacteria. Flushing out the drainage layer this way with lots of fresh water may also help. The plants might also be salvaged if you clean the roots and trim off any pieces that have rotted/died.

However, generally speaking, if you have an enclosure that has stagnated, you’ll need to scrap it and start over. You may be able to bake the soil to kill the bad bacteria and start fresh, but it’ll smell terrible and you’ll just plain be better off using fresh materials. Considering the investment that goes into setting up a bioactive, the best treatment is prevention!


A healthy bioactive setup always smells fresh and earthy – if it doesn’t, that means you have a problem! Although stagnation isn’t always the cause of odor problems, it is one of the #1 killers of a bioactive setup. Having a good substrate is a big part of bioactive, so if you’re new, starting with a pre-made mix like a Bio Dude Bioactive Kit rather than trying to create one yourself is going to maximize your chances of long-term success. However, maintenance is important too: Be mindful of how much you’re watering, and make sure to keep the substrate well aerated!



Hoorman, J. J. (2016, June 6). Role of Soil Bacteria. Ohioline.

Previous Post Next Post

  • Rebekah Walenta


Access Denied

What a shame ----  you do not have permission to view this page : D