After learning how a deep substrate system works in Part One, this is the article where everything becomes real.
This is exactly how I build my own deep substrate tanks — from the first layer of mud to the moment I finally add shrimp and fish. The goal is simple:
Create a tank that becomes more stable and easier to maintain the longer it runs.
If you haven’t read the theory yet, you can start there and come back:
Part One: Deep Substrate Aquariums — Theory, Benefits & How They Work
Once you’re ready to actually get your hands dirty, here’s the process I follow.
✅ What You Need
I keep my setup simple and realistic — things I can usually find locally or online without special brands.
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Mineral soil / mud – the nutrient foundation for roots and microorganisms
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Fine to medium sand – keeps structure, allows gentle oxygen flow
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Leaf litter – food for biofilm, tannins, and natural shelter
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Hardscape (wood + stones) – anchors the layout and gives hiding places
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Root-feeding plants + moss or rhizome plants – the “engine” that uses up nutrients
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Water conditioner – to make tap water safe
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Gentle filter (optional) – for extra clarity and circulation
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Patience – the most important ingredient; this method rewards people who don’t rush
I avoid garden soil with unknown fertilisers or pesticides. If the bag doesn’t clearly say it’s safe for aquariums or ponds, I don’t use it.
✅ Step-By-Step Setup Process
1️⃣ Plan the Layout
Before any soil touches the glass, I spend a few minutes visualising the tank:
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Where will the dense plants grow?
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Where do I want open sand for shrimp and fish to graze?
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Where will the wood and rocks sit so they look natural and don’t block maintenance?
Sometimes I even place the empty hardscape in the dry tank first, just to see how it feels.
A few minutes of planning here can save hours of frustration later.
2️⃣ Bottom Layer — Mineral Soil / Mud
This is the “engine room” of the system.
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Spread 2–3 cm for smaller tanks.
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Go up to 4 cm for larger tanks if you want a very long-term setup.
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Keep the edges against the glass neat so the layers look tidy from the outside.
I gently slope the soil so it’s a bit higher at the back. This gives depth to the layout and more space for plant roots.
Once this layer is down, I try not to disturb it again. It’s the quiet foundation for the whole ecosystem.
3️⃣ Middle Layer — Sand Mixed with Humic Organics
This is where the tank really becomes “alive”.
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Add 2–3 cm of fine to medium sand over the soil.
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Mix in:
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Crushed dried leaves
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Tiny wood fibres
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Optional: a very small amount of peat
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This becomes the bioactive zone:
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Microfauna live here
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Bacteria break down organics
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Roots grow through, carrying oxygen deeper down
I avoid packing this layer too tightly. I want it firm, but still able to breathe.
4️⃣ Hardscape Placement
Next, I place driftwood and stones while the tank is still dry.
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Press them slightly into the sand layer so nothing will float later.
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Think about creating:
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shade and caves for shrimp,
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visual “lines” that guide the eye,
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open areas that won’t be blocked by leaves.
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In deep substrate tanks, hardscape isn’t just decoration — it also helps hold the substrate in place so it doesn’t slide forward over time.
5️⃣ Planting
I like to plant heavily from day one. More plants = more stability.
My usual choices:
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Cryptocoryne – strong root feeders that enjoy rich substrate
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Echinodorus (swords) – big leaves, great nutrient users
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Vallisneria – background grass that spreads with runners
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Rhizome plants attached to wood or rocks:
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Anubias
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Java Fern
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Moss on wood or stones for shrimplets and fry
I plant deep-rooted species straight into the substrate, ensuring the crown is just above the sand, not buried.
This is also the stage where the tank begins to look like a real underwater garden.
6️⃣ Top Layer — Leaf Litter & Moss
Now I add the “forest floor”:
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Lay 1–2 layers of dried leaves loosely over the substrate — not a thick mat
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I use a mix of:
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Catappa
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Guava
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Banana leaf strips
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Add patches of moss in shaded areas for shrimp grazing.
Over time, the leaves:
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Soften
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Grow biofilm
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Break down and gently feed the system
I replace a few leaves every month, but I never strip everything at once. Some old leaf material is part of the ecosystem.
7️⃣ Fill Slowly
This step can make or break your nice clean layers.
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Place a plate, plastic bag, or piece of cling wrap on the substrate.
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Pour water slowly onto that surface, letting it overflow gently.
Some cloudiness is normal, especially in the first few hours or days. I usually:
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Let the filter and plants handle it
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Avoid big water changes unless something looks really wrong
Deep substrate tanks often look a bit “tea-coloured” at first because of tannins — that’s okay.
8️⃣ Cycling (First Month)
This is the part that requires patience.
Instead of thinking “I set up a tank”, I think “I just planted a garden”. Gardens need time.
Here’s roughly what I expect:
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Week 1–2
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Roots start grabbing the substrate.
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A light haze may appear in the water.
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Brown dust on glass or leaves = early diatoms.
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Week 2–4
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Biofilm and microfauna increase.
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Tannins give the water a soft tint.
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Plants show new growth; some older leaves melt and are replaced.
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Week 4+
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Parameters become more stable.
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The tank is usually ready for its first small group of shrimp or fish.
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During this time I:
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Test ammonia and nitrite occasionally.
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Top up evaporation.
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Avoid deep cleaning or heavy vacuuming — I want the layers to settle.
✅ Common Issues & Gentle Fixes
Almost every deep substrate tank goes through some “ugly” stages. Most of them solve themselves if you don’t panic.
Here’s how I read the signs:
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Cloudy water
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Usually normal bacterial bloom early on.
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I leave it for 1–2 weeks unless fish are gasping or something smells bad.
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Early algae
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Too much light or light on for too many hours.
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I reduce intensity or shorten the photoperiod rather than dumping chemicals.
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Gas bubbles trapped under leaves
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Leaf layer may be too thick at the surface.
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I gently lift some leaves to release air and let water flow through.
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Rotten smell from substrate
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This can signal an anaerobic pocket near the surface.
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I:
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Remove excess leaves from that area,
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Increase gentle flow,
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Avoid poking deep down into the layers.
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If something truly smells like sulfur or rotten eggs, I act carefully and don’t stir the whole substrate at once.
🐟 When I Add Fish (and Shrimp)
I only add livestock when I see these signs:
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No ammonia or nitrite during testing
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Water smells clean and earthy, not sharp or rotten
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Plants show strong new growth and firm roots
I start with small, peaceful species that match the natural feel of the tank:
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Rasboras (like hengeli, harlequin)
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Small tetras
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Shrimp and snails as cleaners and grazers
Later, once the system feels solid, a pair of dwarf cichlids (Apistogramma) can also do well, especially with all the leaf litter and hiding spots.
I always stock slowly, giving the system time to adjust between additions.
Final Thoughts
A deep substrate aquarium is not a quick, “instant results” setup. It’s more like planting a miniature forest in a glass box.
Once the foundation is in place and left mostly undisturbed, something special happens:
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The tank becomes more stable with age.
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You spend less time fighting algae and more time just watching behaviour.
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The system begins to support itself in quiet, natural ways.
For me, that’s the real reward of this method — a tank that feels alive, not just maintained.
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