Many hobbyists are concerned that deep substrates are problematic. And indeed thick substrate which traps decomposing organic matter can be an issue as many pathogenic bacteria which cause plant diseases thrive in anaerobic (oxygen-poor) conditions.
Technically not all anaerobic bacteria are 'bad': many provide useful functions such as reducing Ferric Iron from its Fe 3+ state to Ferrous Iron Fe 2+ which is more easily uptake by plants...however in simple terms, we want to avoid having too much anaerobic bacteria.
This said, very thin inert substrates are not ideal for supporting plant growth. The tank above features a very shallow sand substrate. Notice that we do not grow plants in the sandy portions. In the right and left portions of the tank above, aquasoil is used. In fact, the portion on the right has a deep layer of aquasoil substrate- see below.
Most of our readers would know that for plant growth, we recommend aqua soil (raw, organic soil that has been compressed into granules, and distinct from enriched inert substrates that are commonly marketed as aquarium soil). This is because organic soil binds ammonia and acts as store and buffer for nutrients. Rich aqua soil, combined with a leaner fertiliser is one of the secrets to bringing out redder colours in Rotala rotundifolia and its variants (or its red relatives: H'ra / Ceylon / colorata…) due to the effect of nitrate limitation, as described in more detail here.
One of the additional benefits of aqua soil is that due to their large grain size and pore spacing, they do not compact easily even when stacked high. In simple terms, you can have very deep (>10+ inches) aqua soil substrate, and don’t have to worry that the bottom layers gets overly anaerobic.
Aquasoil can be expensive, so if you are creating a slope or an aquascape that requires very deep substrate, it is more cost effective to use an inert material to layer the bottom.
The easiest inert base material to use is perhaps small lava rubble (3-5mm size), as shown above. Lava rock is great for many reasons - it is cheap, widely available, light enough to be easily handled, yet heavy enough to remain at the base. It has good porosity and grain size, and can be used long term and transferred tank to tank without breaking down. Pea gravel or other inert large grain substrates can be used but are probably heavier.
It is also possible to use inert baked clay, with garden soil added on top and finally a layer of aquasoil for easy maintenance (less stirring up of particles during planting, re-planting etc.) This is more complex and is covered in more detail here.
What should I avoid?
It is possible to simply layer with rock and stones, but it is important to first know whether these rocks are truly inert. Limestone such as Seiryu would alter the tank's KH (carbonate hardness) and should be avoided unless you are growing plants that specifically prefer harder water.
Of course, it is important to avoid layering with garden soil that has high organic content, as organic material, if buried too deep, would decompose in anaerobic conditions and create the specific deep-substrate issues we want to avoid.
Finally, fine sands are common and inexpensive, but should not be stacked too deep, as organic debris can easily settle through the fine sand and collect-and start to decompose-at the lower layers. This will cause serious issues if it is stirred up when you do replanting or if you stir up the substrate.
You can have very deep aquasoil substrate with no issues.
If you are layering with rock/ stones, lava rock gravel is an excellent choice.
In general, deep inert layers do not cause problems, unless it has or traps organic content that starts to decompose in anaerobic conditions.