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Should you siphon your aquasoil substrate? Do aquasoils need maintenance?

July 28, 2025 4 min read

Should you siphon your aquasoil substrate? Do aquasoils need maintenance?

Do aquasoils need maintenance?

Aquasoils are now standard in many planted tank setups, but very little information exists on how to maintain them long term. Many aquarists who create short-term setups for photographs or social media treat aquasoil as maintenance-free. However, proper substrate maintenance has a significant impact on algae control and plant health over time.

A well-maintained aquasoil tank doesn't need to be completely torn down for many years.

Two main issues develop over time that aren't immediately apparent to most aquarists. First, organic debris accumulates. Second, the soil's nutrient content depletes.

blood vomit

Aquasoil maintenance is key in higher light tanks to avoid algae and for tanks attempting to propagate more difficult plant species. It is also important for aquarists that to maximize the effectiveness of aquasoil substrates.

Good substrate maintenance allows planted tanks to grow well long term. The aquarium above has substrate that is 1.5 years old.

Clearing organic detritus

Organic detritus is partially decomposed plant matter and animal waste. Over time, it releases nutrients into the substrate. However, too much detritus interferes with root formation and promotes algae growth.

aquarium detritus

Example of a tank with a lot of organic detritus. Delicate plants will not grow well here,  and this is an invitation to algae in higher light tanks.

Low tech aficionados romanticize the idea of organic detritus contributing nutrients to the substrate layer over time, similar to a farmer fertilizing his field with manure. In reality, fish waste is not an effective way to fertilize plants in the aquarium. It does not have a complete nutrient profile and neither does it integrate well into the substrate layer.

Siphon aquasoil

In higher light tanks (150 umols of PAR and above) organic detritus makes a critical difference in algae outcomes. The accumulation of organic detritus is one of the key factors plaguing people with persistent Black beard algae (BBA) problems.

Removing organic debris on the substrate surface can be done together with the weekly water change. This is done by hovering a siphon over the substrate surface while using a turkey baster to scrape up surface debris. For weekly cleaning you should aim to disturb no more than the top 1cm or so of aquasoil. We call this Water Change the 2Hr Way.

Here are a few videos to demonstrate this:

Deep cleaning of substrate and removal of old root systems

Deep cleaning of aquasoil should be in longer intervals, around 8 months to 1 year+ depending on whether there is compaction in the substrate zone. Dense plant growth combined with relatively thin substrate layers is why substrate zones in aquariums get compacted easily. Old roots and fine organic detritus accumulate over the very long time horizon and needs to be cleared for plants to continue to be able to root well. This is similar to repotting terrestrial plants that have outgrown their pots. 

Uproot plants and remove old roots. Siphon away fine organic debris as you uproot the plants to clear compacted zones in the aquasoil.

siphon planted aquarium

Rotala tulunadensis, Rotala florida, and Rotala sunset are all sensitive to substrate quality and cleanliness.

Enriching substrate with ammoniacal nitrogen

Many aquasoils are enriched in ammoniacal nitrogen and this provides a rich source of nitrogen for rooted plants. It is this source of nitrogen that makes plants grown in aquasoil tank larger and more robust compared to plants grown in just inert substrate. Good quality aquasoils will begin to significantly deplete their nitrogen stores after 4 to 6 months. 

2hr aquarist Ludwigia pantanal

Ammonicial nitrogen produces fuller crowns in Ludwigia pantanal (above) and Rotala macrandra (below).

2hr Aquarist Rotala macrandra

Laboratory analysis of aged aquasoil samples from Tom Barr's tanks (Barr Report Vol5, Issue 1) reveals an interesting pattern. While ammonium levels deplete over time, phosphorus, potassium, and iron levels in aged soils are actually higher than in new aquasoils. This is likely due to the high nutrient dosing in the water column of this particular tank, showing that water column nutrients gradually migrate into the substrate. The primary nutrient that needs replenishing as aquasoil ages is ammoniacal nitrogen which depletes over time.

There are two main ways to replenish depleted aquasoils. The first is to use nitrogen-rich root tabs. The second is to add fresh ammonia-rich aquasoil periodically. A good rate is adding 1% of new ammonia-rich aquasoil per month. For example, if you have 30kg of aquasoil in an aquarium, adding around 300 grams per month will work well. You can add new aquasoil during plant replanting cycles. Simply remove a portion of old aquasoil with a water siphon or spoon, then add and mix in the new aquasoil. This method may be cheaper than using root tabs in the long run.

Add new aquasoil
adding new aquasoil
The tank above and below is grown in using 1.5 year old APT Feast, mixed in periodically with new aquasoil.


Clean aquasoil substrate

Ammoniacal nitrogen gives denser, fuller growth to stem plants and gives an edge in propagating picky plant species such as Eriocaulons and Syngonanthus species.

If you do not want to use the add new aquasoil method, our 2hr Aquarist APT Jazz root tabs are designed to be rich in slow release ammoniacal nitrogen for this exact purpose. 

Head here to read on more substrate topics

Head here to read more on water column vs substrate fertilization